| 2006 | 1 | | 8 | FrRnd | 8 | Reds | Drew Stubbs (minors) | 7.4 | 531 | 1940 | 62 | .242 | .698 | | | | | | | 4Yr | University of Texas at Austin (Austin, TX) |
| 2006 | 1 | | 13 | FrRnd | 13 | Cubs | Tyler Colvin (minors) | 2.1 | 357 | 1001 | 44 | .247 | .763 | | | | | | | 4Yr | Clemson University (Clemson, SC) |
| 2006 | 1 | | 14 | FrRnd | 14 | Blue Jays | Travis Snider (minors) | 3.0 | 334 | 1079 | 34 | .250 | .726 | | | | | | | HS | Jackson HS (Jackson, WA) |
| 2006 | 1 | | 15 | FrRnd | 15 | Nationals | Chris Marrero (minors) | -0.7 | 31 | 109 | 0 | .248 | .567 | | | | | | | HS | Monsignor Edward Pace HS (Opa Locka, FL) |
| 2006 | 1 | | 20 | FrRnd | 20 | Twins | Chris Parmelee (minors) | 0.9 | 123 | 387 | 12 | .248 | .722 | | | | | | | HS | Chino Hills HS (Chino Hills, CA) |
| 2006 | 1 | | 24 | FrRnd | 24 | Braves | Cody Johnson (minors) | | | | | | | | | | | | | HS | A. Crawford Mosley HS (Lynn Haven, FL) |
| 2006 | 1 | | 27 | FrRnd | 27 | Red Sox | Jason Place (minors) | | | | | | | | | | | | | HS | Wren HS (Piedmont, SC) |
| 2006 | 1s | | 35 | FrRnd | 35 | Padres | *Kyler Burke (minors) | | | | | | | | | | | | | HS | Ooltewah HS (Ooltewah, TN) |
| 2006 | 2 | | 46 | FrRnd | 2 | Rockies | David Christensen (minors) | | | | | | | | | | | | | HS | Stoneman-Douglas HS (Parkland, FL) |
| 2006 | 2 | | 63 | FrRnd | 19 | Marlins | Thomas Hickman (minors) | | | | | | | | | | | | | HS | Pepperell HS (Lindale, GA) |
| 2006 | 2 | | 64 | FrRnd | 20 | Twins | Joe Benson (minors) | -0.6 | 21 | 71 | 0 | .239 | .622 | | | | | | | HS | Joliet Catholic Academy (Joliet, IL) |
| 2006 | 2 | | 70 | FrRnd | 26 | Nationals via Angels | *Stephen Englund (minors) | | | | | | | | | | | | | HS | Bellevue HS (Bellevue, WA) |
| 2006 | 2 | | 74 | FrRnd | 30 | Cardinals | Jon Jay (minors) | 7.7 | 425 | 1343 | 22 | .298 | .772 | | | | | | | 4Yr | University of Miami (Coral Gables, FL) |
| 2006 | 3 | | 82 | FrRnd | 6 | Tigers | Brennan Boesch (minors) | 2.1 | 400 | 1405 | 44 | .258 | .728 | | | | | | | 4Yr | University of California, Berkeley (Berkeley, CA) |
| 2006 | 3 | | 87 | FrRnd | 11 | Diamondbacks | Cyle Hankerd (minors) | | | | | | | | | | | | | 4Yr | University of Southern California (Los Angeles, CA) |
| 2006 | 3 | | 92 | FrRnd | 16 | Brewers | Cole Gillespie (minors) | -0.6 | 50 | 110 | 3 | .236 | .683 | | | | | | | 4Yr | Oregon State University (Corvallis, OR) |
| 2006 | 3 | | 93 | FrRnd | 17 | Padres | Cedric Hunter (minors) | -0.0 | 6 | 4 | 0 | .250 | .650 | | | | | | | HS | Martin Luther King HS (Lithonia, GA) |
| 2006 | 3 | | 95 | FrRnd | 19 | Marlins | Scott Cousins (minors) | -0.5 | 135 | 179 | 2 | .179 | .515 | | | | | | | 4Yr | University of San Francisco (San Francisco, CA) |
| 2006 | 3 | | 98 | FrRnd | 22 | Athletics | Matthew Sulentic (minors) | | | | | | | | | | | | | HS | Hillcrest HS (Hillcrest, TX) |
| 2006 | 3 | | 99 | FrRnd | 23 | Astros | Nicholas Moresi (minors) | | | | | | | | | | | | | 4Yr | California State University Fresno (Fresno, CA) |
| 2006 | 3 | | 102 | FrRnd | 26 | Angels | Russell Moldenhauer (minors) | | | | | | | | | | | | | HS | Boerne HS (Fair Oaks Ranch, TX) |
| 2006 | 4 | | 107 | FrRnd | 1 | Royals | Derrick Robinson (minors) | 0.3 | 27 | 32 | 0 | .281 | .676 | | | | | | | HS | P.K. Yonge Developmental Research School (Gainesville, FL) |
| 2006 | 4 | | 114 | FrRnd | 8 | Reds | Justin Reed (minors) | | | | | | | | | | | | | HS | Hillcrest Christian HS (Jackson, MS) |
| 2006 | 4 | | 127 | FrRnd | 21 | Phillies | D'Arby Myers (minors) | | | | | | | | | | | | | HS | Westchester HS (Los Angeles, CA) |
| 2006 | 4 | | 132 | FrRnd | 26 | Angels | Clay Fuller (minors) | | | | | | | | | | | | | HS | Smithson Valley HS (Spring Branch, TX) |
| 2006 | 4 | | 134 | FrRnd | 28 | Yankees | Colin Curtis (minors) | -0.3 | 31 | 59 | 1 | .186 | .538 | | | | | | | 4Yr | Arizona State University (Tempe, AZ) |
| 2006 | 5 | | 146 | FrRnd | 10 | Giants | Mike McBryde (minors) | | | | | | | | | | | | | 4Yr | Florida Atlantic University (Boca Raton, FL) |
| 2006 | 5 | | 152 | FrRnd | 16 | Brewers | Chris Errecart (minors) | | | | | | | | | | | | | 4Yr | University of California, Berkeley (Berkeley, CA) |
| 2006 | 5 | | 156 | FrRnd | 20 | Twins | Devin Shepherd (minors) | | | | | | | | | | | | | HS | Oxnard HS (Oxnard, CA) |
| 2006 | 5 | | 157 | FrRnd | 21 | Phillies | Quintin Berry (minors) | 0.5 | 94 | 291 | 2 | .258 | .684 | | | | | | | 4Yr | San Diego State University (San Diego, CA) |
| 2006 | 5 | | 158 | FrRnd | 22 | Athletics | Jermaine Mitchell (minors) | | | | | | | | | | | | | 4Yr | University of North Carolina at Greensboro (Greensboro, NC) |
| 2006 | 5 | | 166 | FrRnd | 30 | Cardinals | Shane Robinson (minors) | 0.4 | 148 | 232 | 3 | .233 | .615 | | | | | | | 4Yr | Florida State University (Tallahassee, FL) |
| 2006 | 6 | | 168 | FrRnd | 2 | Rockies | Kevin Clark (minors) | | | | | | | | | | | | | JC | Manatee Community College (Bradenton, FL) |
| 2006 | 6 | | 177 | FrRnd | 11 | Diamondbacks | Joey Side (minors) | | | | | | | | | | | | | 4Yr | University of Georgia (Athens, GA) |
| 2006 | 7 | | 197 | FrRnd | 1 | Royals | Brett Bigler (minors) | | | | | | | | | | | | | 4Yr | University of California, Riverside (Riverside, CA) |
| 2006 | 7 | | 200 | FrRnd | 4 | Pirates | Austin McClune (minors) | | | | | | | | | | | | | HS | Edmond Santa Fe HS (Edmond, OK) |
| 2006 | 7 | | 208 | FrRnd | 12 | Rangers | Grant Gerrard (minors) | | | | | | | | | | | | | 4Yr | Southern Illinois University Carbondale (Carbondale, IL) |
| 2006 | 7 | | 210 | FrRnd | 14 | Blue Jays | Jonathan Baksh (minors) | | | | | | | | | | | | | | |
| 2006 | 7 | | 214 | FrRnd | 18 | Mets | Daniel Stegall (minors) | | | | | | | | | | | | | HS | Greenwood HS (Greenwood, AR) |
| 2006 | 7 | | 222 | FrRnd | 26 | Angels | Jarrad Page (minors) | | | | | | | | | | | | | 4Yr | University of California, Los Angeles (Los Angeles, CA) |
| 2006 | 7 | | 226 | FrRnd | 30 | Cardinals | Luke Gorsett (minors) | | | | | | | | | | | | | 4Yr | University of Nebraska at Lincoln (Lincoln, NE) |
| 2006 | 8 | | 230 | FrRnd | 4 | Pirates | Alex Presley (minors) | 1.1 | 180 | 587 | 14 | .261 | .724 | | | | | | | 4Yr | University of Mississippi (Oxford, MS) |
| 2006 | 8 | | 233 | FrRnd | 7 | Dodgers | Tommy Giles (minors) | | | | | | | | | | | | | 4Yr | University of Miami (Coral Gables, FL) |
| 2006 | 8 | | 238 | FrRnd | 12 | Rangers | Josh Bradbury (minors) | | | | | | | | | | | | | JC | Orange Coast College (Costa Mesa, CA) |
| 2006 | 8 | | 247 | FrRnd | 21 | Phillies | T.J. Warren (minors) | | | | | | | | | | | | | HS | Jesse M. Bethel HS (Vallejo, CA) |
| 2006 | 8 | | 248 | FrRnd | 22 | Athletics | Angel Sierra (minors) | | | | | | | | | | | | | HS | Puerto Rico Baseball Academy (Gurabo, PR) |
| 2006 | 8 | | 249 | FrRnd | 23 | Astros | Jimmy Van Ostrand (minors) | | | | | | | | | | | | | 4Yr | California Polytechnic State University, San Luis Obispo (San Luis Obispo, CA) |
| 2006 | 8 | | 253 | FrRnd | 27 | Red Sox | Rafael Cabreja (minors) | | | | | | | | | | | | | HS | James Monroe HS (Bronx, NY) |
| 2006 | 8 | | 255 | FrRnd | 29 | White Sox | Kent Gerst (minors) | | | | | | | | | | | | | HS | Fort Zumwalt West (O'Fallon, MO) |
| 2006 | 9 | | 269 | FrRnd | 13 | Cubs | Cliff Andersen (minors) | | | | | | | | | | | | | HS | Cottonwood HS (Salt Lake City, UT) |
| 2006 | 9 | | 274 | FrRnd | 18 | Mets | Jeremy Barfield (minors) | | | | | | | | | | | | | HS | Klein HS (Klein, TX) |
| 2006 | 9 | | 275 | FrRnd | 19 | Marlins | John Raynor (minors) | -0.0 | 11 | 10 | 0 | .200 | .473 | | | | | | | 4Yr | University of North Carolina at Wilmington (Wilmington, NC) |
| 2006 | 9 | | 283 | FrRnd | 27 | Red Sox | Ryan Kalish (minors) | -0.1 | 89 | 259 | 4 | .243 | .644 | | | | | | | HS | Red Bank Catholic HS (Red Bank, NJ) |
| 2006 | 10 | | 287 | FrRnd | 1 | Royals | Nick Van Stratten (minors) | | | | | | | | | | | | | JC | St. Louis Community College, Meramec Campus (Kirkwood, MO) |
| 2006 | 10 | | 289 | FrRnd | 3 | Devil Rays | Desmond Jennings (minors) | 6.8 | 255 | 947 | 28 | .246 | .726 | | | | | | | JC | Itawamba Community College (Fulton, MS) |
| 2006 | 10 | | 295 | FrRnd | 9 | Orioles | Emeel Salem (minors) | | | | | | | | | | | | | 4Yr | University of Alabama (Tuscaloosa, AL) |
| 2006 | 10 | | 298 | FrRnd | 12 | Rangers | Craig Gentry (minors) | 5.2 | 250 | 502 | 3 | .275 | .700 | 1 | 0 | 0 | 18.00 | 4.00 | 0 | 4Yr | University of Arkansas (Fayetteville, AR) |
| 2006 | 10 | | 306 | FrRnd | 20 | Twins | Jared Mitchell (minors) | | | | | | | | | | | | | HS | Westgate HS (New Iberia, LA) |
| 2006 | 10 | | 315 | FrRnd | 29 | White Sox | Lee Cruz (minors) | | | | | | | | | | | | | 4Yr | University of Tampa (Tampa, FL) |
| 2006 | 11 | | 318 | FrRnd | 2 | Rockies | Aaron Miller (minors) | | | | | | | | | | | | | HS | Channelview HS (Channelview, TX) |
| 2006 | 11 | | 332 | FrRnd | 16 | Brewers | Zach Clem (minors) | | | | | | | | | | | | | 4Yr | University of Washington (Seattle, WA) |
| 2006 | 11 | | 343 | FrRnd | 27 | Red Sox | Brandon Belt (minors) | 4.8 | 253 | 741 | 22 | .258 | .760 | | | | | | | HS | Hudson HS (Lufkin, TX) |
| 2006 | 11 | | 344 | FrRnd | 28 | Yankees | Seth Fortenberry (minors) | | | | | | | | | | | | | 4Yr | Baylor University (Waco, TX) |
| 2006 | 12 | | 351 | FrRnd | 5 | Mariners | Gavin Dickey (minors) | | | | | | | | | | | | | 4Yr | University of Florida (Gainesville, FL) |
| 2006 | 12 | | 355 | FrRnd | 9 | Orioles | Brandon Tripp (minors) | | | | | | | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 2006 | 12 | | 356 | FrRnd | 10 | Giants | Matt Weston (minors) | | | | | | | | | | | | | 4Yr | University of Houston (Houston, TX) |
| 2006 | 12 | | 366 | FrRnd | 20 | Twins | Kevin Harrington (minors) | | | | | | | | | | | | | HS | Royal HS (Simi Valley, CA) |
| 2006 | 12 | | 367 | FrRnd | 21 | Phillies | Darin McDonald (minors) | | | | | | | | | | | | | HS | Cherry Creek HS (Englewood, CO) |
| 2006 | 12 | | 375 | FrRnd | 29 | White Sox | Sergio Morales (minors) | | | | | | | | | | | | | JC | Broward Community College (Fort Lauderdale, FL) |
| 2006 | 13 | | 389 | FrRnd | 13 | Cubs | Matt Camp (minors) | | | | | | | | | | | | | 4Yr | North Carolina State University (Raleigh, NC) |
| 2006 | 13 | | 390 | FrRnd | 14 | Blue Jays | Mikal Garbarino (minors) | | | | | | | | | | | | | HS | San Dimas HS (San Dimas, CA) |
| 2006 | 13 | | 393 | FrRnd | 17 | Padres | Michael Epping (minors) | | | | | | | | | | | | | 4Yr | University of New Orleans (New Orleans, LA) |
| 2006 | 13 | | 396 | FrRnd | 20 | Twins | Aaron Senne (minors) | | | | | | | | | | | | | HS | Mayo HS (Rochester, MN) |
| 2006 | 13 | | 406 | FrRnd | 30 | Cardinals | Travis Mitchell (minors) | | | | | | | | | | | | | HS | Parkway Central HS (Chesterfield, MO) |
| 2006 | 14 | | 408 | FrRnd | 2 | Rockies | Jeff Kindel (minors) | | | | | | | | | | | | | 4Yr | Georgia Institute of Technology (Atlanta, GA) |
| 2006 | 14 | | 414 | FrRnd | 8 | Reds | Carson Kainer (minors) | | | | | | | | | | | | | 4Yr | University of Texas at Austin (Austin, TX) |
| 2006 | 14 | | 419 | FrRnd | 13 | Cubs | Drew Rundle (minors) | | | | | | | | | | | | | HS | Bend HS (Bend, OR) |
| 2006 | 14 | | 420 | FrRnd | 14 | Blue Jays | Shawn Scobee (minors) | | | | | | | | | | | | | 4Yr | University of Nevada-Reno (Reno, NV) |
| 2006 | 14 | | 427 | FrRnd | 21 | Phillies | Gus Milner (minors) | | | | | | | | | | | | | 4Yr | University of Kansas (Lawrence, KS) |
| 2006 | 14 | | 428 | FrRnd | 22 | Athletics | Todd Johnson (minors) | | | | | | | | | | | | | 4Yr | University of Southern Mississippi (Hattiesburg, MS) |
| 2006 | 14 | | 434 | FrRnd | 28 | Yankees | D.J. Hollingsworth (minors) | | | | | | | | | | | | | 4Yr | University of California, Riverside (Riverside, CA) |
| 2006 | 14 | | 436 | FrRnd | 30 | Cardinals | Jon Edwards (minors) | | | | | | | | | | | | | HS | Keller HS (Keller, TX) |
| 2006 | 15 | | 437 | FrRnd | 1 | Royals | Nick Francis (minors) | | | | | | | | | | | | | JC | Pensacola Junior College (Pensacola, FL) |
| 2006 | 15 | | 438 | FrRnd | 2 | Rockies | Victor Ferrante (minors) | | | | | | | | | | | | | JC | Solano Community College (Fairfield, CA) |
| 2006 | 15 | | 439 | FrRnd | 3 | Devil Rays | Kyeong Kang (minors) | | | | | | | | | | | | | HS | Parkview HS (Lilburn, GA) |
| 2006 | 15 | | 440 | FrRnd | 4 | Pirates | James Barksdale (minors) | | | | | | | | | | | | | 4Yr | University of North Alabama (Florence, AL) |
| 2006 | 15 | | 456 | FrRnd | 20 | Twins | Mark Dolenc (minors) | | | | | | | | | | | | | 4Yr | Minnesota State University, Mankato (Mankato, MN) |
| 2006 | 15 | | 457 | FrRnd | 21 | Phillies | Riley Cooper (minors) | | | | | | | | | | | | | HS | Clearwater Central Catholic HS (Clearwater, FL) |
| 2006 | 16 | | 468 | FrRnd | 2 | Rockies | Anthony Jackson (minors) | | | | | | | | | | | | | 4Yr | University of the Pacific (Stockton, CA) |
| 2006 | 16 | | 478 | FrRnd | 12 | Rangers | Cody Podraza (minors) | | | | | | | | | | | | | HS | Tomball HS (Tomball, TX) |
| 2006 | 16 | | 486 | FrRnd | 20 | Twins | Shayne Willson (minors) | | | | | | | | | | | | | HS | Earl Marriott SS (Surrey, BC) |
| 2006 | 16 | | 489 | FrRnd | 23 | Astros | Drew Holder (minors) | | | | | | | | | | | | | 4Yr | Dallas Baptist University (Dallas, TX) |
| 2006 | 16 | | 491 | FrRnd | 25 | Indians | Stephen Douglas (minors) | | | | | | | | | | | | | 4Yr | East Tennessee State University (Johnson City, TN) |
| 2006 | 17 | | 499 | FrRnd | 3 | Devil Rays | Ryan Thornton (minors) | | | | | | | | | | | | | JC | American River College (Sacramento, CA) |
| 2006 | 17 | | 504 | FrRnd | 8 | Reds | Chris Heisey (minors) | 2.1 | 360 | 902 | 35 | .252 | .732 | | | | | | | 4Yr | Messiah College (Grantham, PA) |
| 2006 | 17 | | 515 | FrRnd | 19 | Marlins | Hunter Mense (minors) | | | | | | | | | | | | | 4Yr | University of Missouri Columbia (Columbia, MO) |
| 2006 | 17 | | 517 | FrRnd | 21 | Phillies | Jay Miller (minors) | | | | | | | | | | | | | 4Yr | Washington State University (Pullman, WA) |
| 2006 | 17 | | 523 | FrRnd | 27 | Red Sox | Josh Reddick (minors) | 6.3 | 328 | 1078 | 43 | .237 | .725 | | | | | | | JC | Middle Georgia College (Cochran, GA) |
| 2006 | 17 | | 526 | FrRnd | 30 | Cardinals | Nathan Southard (minors) | | | | | | | | | | | | | 4Yr | Tulane University (New Orleans, LA) |
| 2006 | 18 | | 527 | FrRnd | 1 | Royals | Chase Larsson (minors) | | | | | | | | | | | | | HS | Kitsilano SS (Vancouver, BC) |
| 2006 | 18 | | 532 | FrRnd | 6 | Tigers | Deik Scram (minors) | | | | | | | | | | | | | 4Yr | Oklahoma State University (Stillwater, OK) |
| 2006 | 18 | | 543 | FrRnd | 17 | Padres | Garner Wetzel (minors) | | | | | | | | | | | | | 4Yr | Millsaps College (Jackson, MS) |
| 2006 | 18 | | 551 | FrRnd | 25 | Indians | Daryl King (minors) | | | | | | | | | | | | | HS | Benicia HS (Benicia, CA) |
| 2006 | 18 | | 556 | FrRnd | 30 | Cardinals | Amaury Cazana (minors) | | | | | | | | | | | | | | |
| 2006 | 19 | | 560 | FrRnd | 4 | Pirates | Jason Moseby (minors) | | | | | | | | | | | | | HS | Newport HS (Bellevue, WA) |
| 2006 | 19 | | 566 | FrRnd | 10 | Giants | Tyler Graham (minors) | -0.1 | 10 | 2 | 0 | .000 | .000 | | | | | | | 4Yr | Oregon State University (Corvallis, OR) |
| 2006 | 19 | | 567 | FrRnd | 11 | Diamondbacks | Tyler Jones (minors) | | | | | | | | | | | | | 4Yr | University of South Alabama (Mobile, AL) |
| 2006 | 19 | | 568 | FrRnd | 12 | Rangers | Miguel Velazquez (minors) | | | | | | | | | | | | | HS | Gabriela Mistral HS (San Juan, PR) |
| 2006 | 19 | | 572 | FrRnd | 16 | Brewers | Lee Haydel (minors) | | | | | | | | | | | | | | |
| 2006 | 19 | | 579 | FrRnd | 23 | Astros | Orlando Rosales (minors) | | | | | | | | | | | | | 4Yr | University of Tampa (Tampa, FL) |
| 2006 | 19 | | 582 | FrRnd | 26 | Angels | Chris Pettit (minors) | -0.1 | 11 | 7 | 0 | .286 | .571 | | | | | | | 4Yr | Loyola Marymount University (Los Angeles, CA) |
| 2006 | 20 | | 603 | FrRnd | 17 | Padres | Michael Campbell (minors) | | | | | | | | | | | | | 4Yr | University of South Carolina (Columbia, SC) |
| 2006 | 20 | | 605 | FrRnd | 19 | Marlins | Steven Sultzbaugh (minors) | | | | | | | | | | | | | HS | Westwood HS (Austin, TX) |
| 2006 | 20 | | 610 | FrRnd | 24 | Braves | Jonathan Cluff (minors) | | | | | | | | | | | | | HS | Bingham HS (South Jordan, UT) |
| 2006 | 21 | | 623 | FrRnd | 7 | Dodgers | Matt Berezay (minors) | | | | | | | | | | | | | 4Yr | University of the Pacific (Stockton, CA) |
| 2006 | 21 | | 625 | FrRnd | 9 | Orioles | Luis Lopez (minors) | | | | | | | | | | | | | HS | Dra Maria Cadilla HS (Arecibo, PR) |
| 2006 | 21 | | 631 | FrRnd | 15 | Nationals | Christopher French (minors) | | | | | | | | | | | | | JC | New Mexico Junior College (Hobbs, NM) |
| 2006 | 21 | | 633 | FrRnd | 17 | Padres | Luke Cannon (minors) | | | | | | | | | | | | | 4Yr | Texas State University (San Marcos, TX) |
| 2006 | 21 | | 637 | FrRnd | 21 | Phillies | Jacob Dempsey (minors) | | | | | | | | | | | | | 4Yr | Winthrop University (Rock Hill, SC) |
| 2006 | 21 | | 642 | FrRnd | 26 | Angels | John Vincent (minors) | | | | | | | | | | | | | 4Yr | New Mexico State University (Las Cruces, NM) |
| 2006 | 22 | | 648 | FrRnd | 2 | Rockies | Jay Cox (minors) | | | | | | | | | | | | | 4Yr | University of North Carolina at Chapel Hill (Chapel Hill, NC) |
| 2006 | 22 | | 650 | FrRnd | 4 | Pirates | Miles Durham (minors) | | | | | | | | | | | | | 4Yr | Northwestern State University of Louisiana (Natchitoches, LA) |
| 2006 | 22 | | 653 | FrRnd | 7 | Dodgers | Christopher Jensen (minors) | | | | | | | | | | | | | 4Yr | University of California, Los Angeles (Los Angeles, CA) |
| 2006 | 22 | | 656 | FrRnd | 10 | Giants | Bobby Felmy (minors) | | | | | | | | | | | | | 4Yr | University of Georgia (Athens, GA) |
| 2006 | 22 | | 657 | FrRnd | 11 | Diamondbacks | Danny Perales (minors) | | | | | | | | | | | | | 4Yr | University of Southern California (Los Angeles, CA) |
| 2006 | 22 | | 674 | FrRnd | 28 | Yankees | Brian Aragon (minors) | | | | | | | | | | | | | 4Yr | North Carolina State University (Raleigh, NC) |
| 2006 | 23 | | 679 | FrRnd | 3 | Devil Rays | Matthew McCarney (minors) | | | | | | | | | | | | | HS | Holy Trinity Catholic HS (Kanata, ON) |
| 2006 | 23 | | 684 | FrRnd | 8 | Reds | Tony Brown (minors) | | | | | | | | | | | | | HS | Crestview HS (Crestview, FL) |
| 2006 | 23 | | 687 | FrRnd | 11 | Diamondbacks | Derrick Walker (minors) | | | | | | | | | | | | | JC | Wabash Valley College (Mount Carmel, IL) |
| 2006 | 23 | | 690 | FrRnd | 14 | Blue Jays | Adam Calderone (minors) | | | | | | | | | | | | | 4Yr | Florida Southern College (Lakeland, FL) |
| 2006 | 23 | | 703 | FrRnd | 27 | Red Sox | Paul Smyth (minors) | | | | | | | | | | | | | 4Yr | San Diego State University (San Diego, CA) |
| 2006 | 24 | | 712 | FrRnd | 6 | Tigers | Joseph Tucker (minors) | | | | | | | | | | | | | 4Yr | Kent State University (Kent, OH) |
| 2006 | 24 | | 717 | FrRnd | 11 | Diamondbacks | Andrew Beshenich (minors) | | | | | | | | | | | | | HS | Norristown HS (Norristown, PA) |
| 2006 | 24 | | 725 | FrRnd | 19 | Marlins | Ernesto Rivera (minors) | | | | | | | | | | | | | HS | Puerto Rico Baseball Academy (Gurabo, PR) |
| 2006 | 25 | | 738 | FrRnd | 2 | Rockies | Jeremy Jones (minors) | | | | | | | | | | | | | 4Yr | North Carolina A&T State University (Greensboro, NC) |
| 2006 | 25 | | 741 | FrRnd | 5 | Mariners | Tyson Gillies (minors) | | | | | | | | | | | | | HS | R. E. Mountain Secondary (Langley, BC) |
| 2006 | 25 | | 744 | FrRnd | 8 | Reds | Michael McKennon (minors) | | | | | | | | | | | | | 4Yr | University of Texas at San Antonio (San Antonio, TX) |
| 2006 | 25 | | 747 | FrRnd | 11 | Diamondbacks | Shane Byrne (minors) | | | | | | | | | | | | | 4Yr | East Tennessee State University (Johnson City, TN) |
| 2006 | 25 | | 752 | FrRnd | 16 | Brewers | Mike Goetz (minors) | | | | | | | | | | | | | 4Yr | University of Wisconsin at Milwaukee (Milwaukee, WI) |
| 2006 | 25 | | 765 | FrRnd | 29 | White Sox | Joe Hunter (minors) | | | | | | | | | | | | | 4Yr | Mississippi State University (Mississippi State, MS) |
| 2006 | 25 | | 766 | FrRnd | 30 | Cardinals | D'Marcus Ingram (minors) | | | | | | | | | | | | | HS | North Little Rock HS (North Little Rock, AR) |
| 2006 | 26 | | 767 | FrRnd | 1 | Royals | Darrell Lockett (minors) | | | | | | | | | | | | | HS | Weatherford HS (Weatherford, TX) |
| 2006 | 26 | | 772 | FrRnd | 6 | Tigers | Daniel Renfroe (minors) | | | | | | | | | | | | | HS | Tattnall Square Academy (Macon, GA) |
| 2006 | 26 | | 775 | FrRnd | 9 | Orioles | Kipp Schutz (minors) | | | | | | | | | | | | | HS | Harrison HS (Evansville, IN) |
| 2006 | 26 | | 780 | FrRnd | 14 | Blue Jays | Chris Emanuele (minors) | | | | | | | | | | | | | 4Yr | Northeastern University (Boston, MA) |
| 2006 | 26 | | 784 | FrRnd | 18 | Mets | Dustin Martin (minors) | | | | | | | | | | | | | 4Yr | Sam Houston State University (Huntsville, TX) |
| 2006 | 27 | | 799 | FrRnd | 3 | Devil Rays | Luis Lopez (minors) | | | | | | | | | | | | | HS | St. Francis School (Carolina, PR) |
| 2006 | 27 | | 804 | FrRnd | 8 | Reds | Kel Jones (minors) | | | | | | | | | | | | | JC | Darton CC (Albany, GA) |
| 2006 | 27 | | 806 | FrRnd | 10 | Giants | Sean VanElderen (minors) | | | | | | | | | | | | | JC | Mesa State College (Grand Junction, CO) |
| 2006 | 27 | | 807 | FrRnd | 11 | Diamondbacks | Connor Janes (minors) | | | | | | | | | | | | | 4Yr | University of British Columbia (Vancouver, BC) |
| 2006 | 27 | | 818 | FrRnd | 22 | Athletics | Larry Cobb (minors) | | | | | | | | | | | | | 4Yr | College of Charleston (Charleston, SC) |
| 2006 | 27 | | 821 | FrRnd | 25 | Indians | Christopher Roberts (minors) | | | | | | | | | | | | | HS | Oshkosh West HS (Oshkosh, WI) |
| 2006 | 28 | | 827 | FrRnd | 1 | Royals | Michael Wheeler (minors) | | | | | | | | | | | | | JC | Walters State Community College (Morristown, TN) |
| 2006 | 28 | | 829 | FrRnd | 3 | Devil Rays | Andrew Hagins (minors) | | | | | | | | | | | | | HS | Oak Park & River Forest HS (Oak Park, y) |
| 2006 | 28 | | 836 | FrRnd | 10 | Giants | Dusty Harvard (minors) | | | | | | | | | | | | | HS | Natrona County HS (Natrona County, WY) |
| 2006 | 28 | | 842 | FrRnd | 16 | Brewers | Terrell Alliman (minors) | | | | | | | | | | | | | HS | Bluevale Collegiate Institute (Waterloo, ON) |
| 2006 | 28 | | 844 | FrRnd | 18 | Mets | Will Bashelor (minors) | | | | | | | | | | | | | 4Yr | Dartmouth College (Hanover, NH) |
| 2006 | 28 | | 848 | FrRnd | 22 | Athletics | Lorenzo Macias (minors) | | | | | | | | | | | | | JC | Mount San Antonio College (Walnut, CA) |
| 2006 | 28 | | 850 | FrRnd | 24 | Braves | Adam Milligan (minors) | | | | | | | | | | | | | HS | Hardin County HS (Selmer, TN) |
| 2006 | 29 | | 859 | FrRnd | 3 | Devil Rays | Leon Johnson (minors) | | | | | | | | | | | | | | |
| 2006 | 29 | | 870 | FrRnd | 14 | Blue Jays | Ryan Basham (minors) | | | | | | | | | | | | | 4Yr | Michigan State University (East Lansing, MI) |
| 2006 | 29 | | 871 | FrRnd | 15 | Nationals | Khris Davis (minors) | -0.2 | 14 | 16 | 0 | .188 | .590 | | | | | | | HS | Deer Valley HS (Glendale, AZ) |
| 2006 | 29 | | 879 | FrRnd | 23 | Astros | Rafeal Parks (minors) | | | | | | | | | | | | | HS | Greenbrier HS (Greenbrier, GA) |
| 2006 | 30 | | 888 | FrRnd | 2 | Rockies | Scott Robinson (minors) | | | | | | | | | | | | | HS | Henry County HS (Henry County, GA) |
| 2006 | 30 | | 890 | FrRnd | 4 | Pirates | Alphonso Owens (minors) | | | | | | | | | | | | | HS | Dillon HS (Dillon, SC) |
| 2006 | 30 | | 892 | FrRnd | 6 | Tigers | Phil Ortez (minors) | | | | | | | | | | | | | JC | Scottsdale Community College (Scottsdale, AZ) |
| 2006 | 30 | | 907 | FrRnd | 21 | Phillies | Brian Capps (minors) | | | | | | | | | | | | | 4Yr | Texas Tech University (Lubbock, TX) |
| 2006 | 30 | | 910 | FrRnd | 24 | Braves | David Berres (minors) | | | | | | | | | | | | | JC | South Suburban College (South Holland, IL) |
| 2006 | 31 | | 918 | FrRnd | 2 | Rockies | Curtis Dupart (minors) | | | | | | | | | | | | | HS | Woodinville HS (Woodinville, WA) |
| 2006 | 31 | | 919 | FrRnd | 3 | Devil Rays | Justin Reynolds (minors) | | | | | | | | | | | | | JC | Mount Hood Community College (Gresham, OR) |
| 2006 | 31 | | 922 | FrRnd | 6 | Tigers | Mike Sullivan (minors) | | | | | | | | | | | | | 4Yr | Ball State University (Muncie, IN) |
| 2006 | 31 | | 934 | FrRnd | 18 | Mets | Jeremy Hambrice (minors) | | | | | | | | | | | | | 4Yr | Southern Arkansas University (Magnolia, AR) |
| 2006 | 31 | | 935 | FrRnd | 19 | Marlins | William Mays (minors) | | | | | | | | | | | | | JC | Sinclair Community College (Dayton, OH) |
| 2006 | 31 | | 938 | FrRnd | 22 | Athletics | Jonathan Pigott (minors) | | | | | | | | | | | | | HS | Seabreeze HS (Daytona Beach, FL) |
| 2006 | 31 | | 943 | FrRnd | 27 | Red Sox | Logan Schafer (minors) | 0.4 | 61 | 71 | 0 | .225 | .592 | | | | | | | JC | Cuesta College (San Luis Obispo, CA) |
| 2006 | 31 | | 944 | FrRnd | 28 | Yankees | Zakary Presley (minors) | | | | | | | | | | | | | HS | Carroll HS (Southlake, TX) |
| 2006 | 31 | | 945 | FrRnd | 29 | White Sox | Stefan Gartrell (minors) | | | | | | | | | | | | | 4Yr | University of San Francisco (San Francisco, CA) |
| 2006 | 31 | | 946 | FrRnd | 30 | Cardinals | Mark Shorey (minors) | | | | | | | | | | | | | 4Yr | High Point University (High Point, NC) |
| 2006 | 32 | | 949 | FrRnd | 3 | Devil Rays | Emmanuel Morales (minors) | | | | | | | | | | | | | HS | Puerto Rico Baseball Academy (Gurabo, PR) |
| 2006 | 32 | | 954 | FrRnd | 8 | Reds | Danny Dorn (minors) | | | | | | | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 2006 | 32 | | 976 | FrRnd | 30 | Cardinals | Ross Smith (minors) | | | | | | | | | | | | | HS | Dodge County HS (Milan, GA) |
| 2006 | 33 | | 977 | FrRnd | 1 | Royals | Harold Smith (minors) | | | | | | | | | | | | | HS | Miami Palmetto Senior HS (Miami, FL) |
| 2006 | 33 | | 988 | FrRnd | 12 | Rangers | Eric Fry (minors) | | | | | | | | | | | | | JC | San Jacinto College (Pasadena, TX) |
| 2006 | 33 | | 999 | FrRnd | 23 | Astros | Codi Harshman (minors) | | | | | | | | | | | | | HS | Sabino HS (Tucson, AZ) |
| 2006 | 33 | | 1001 | FrRnd | 25 | Indians | Jarett Jackson (minors) | | | | | | | | | | | | | HS | Thomas Jefferson HS (Auburn, WA) |
| 2006 | 33 | | 1005 | FrRnd | 29 | White Sox | Chris Ulrey (minors) | | | | | | | | | | | | | HS | New Palestine HS (New Palestine, IN) |
| 2006 | 34 | | 1011 | FrRnd | 5 | Mariners | Stanley Posluszny (minors) | | | | | | | | | | | | | 4Yr | West Virginia University (Morgantown, WV) |
| 2006 | 34 | | 1013 | FrRnd | 7 | Dodgers | Luke Yoder (minors) | | | | | | | | | | | | | HS | Liberty HS (Liberty, CA) |
| 2006 | 34 | | 1021 | FrRnd | 15 | Nationals | Taylor Kinzer (minors) | | | | | | | | | | | | | HS | Homestead HS (Fort Wayne, IN) |
| 2006 | 34 | | 1032 | FrRnd | 26 | Angels | Bobby Wagner (minors) | | | | | | | | | | | | | JC | Douglas College (New Westminster, BC) |
| 2006 | 34 | | 1035 | FrRnd | 29 | White Sox | Ty Wright (minors) | | | | | | | | | | | | | JC | South Florida Community College (Avon Park, FL) |
| 2006 | 35 | | 1043 | FrRnd | 7 | Dodgers | Nick Buss (minors) | | | | | | | | | | | | | JC | San Diego Mesa College (San Diego, CA) |
| 2006 | 35 | | 1048 | FrRnd | 12 | Rangers | Brian Nelson (minors) | | | | | | | | | | | | | 4Yr | Western Baptist College (Salem, OR) |
| 2006 | 35 | | 1051 | FrRnd | 15 | Nationals | D' Vontrey Richardson (minors) | | | | | | | | | | | | | HS | Lee County HS (Leesburg, GA) |
| 2006 | 35 | | 1057 | FrRnd | 21 | Phillies | Rashad Taylor (minors) | | | | | | | | | | | | | JC | Skyline JC (San Bruno, CA) |
| 2006 | 35 | | 1059 | FrRnd | 23 | Astros | Patrick Allen (minors) | | | | | | | | | | | | | JC | Everett Community College (Everett, WA) |
| 2006 | 35 | | 1063 | FrRnd | 27 | Red Sox | Jeremy Rahman (minors) | | | | | | | | | | | | | HS | Hazelwood Central HS (Florissant, MO) |
| 2006 | 35 | | 1065 | FrRnd | 29 | White Sox | Adam Heisler (minors) | | | | | | | | | | | | | HS | Baker HS (Mobile, AL) |
| 2006 | 35 | | 1066 | FrRnd | 30 | Cardinals | Jim Rapoport (minors) | | | | | | | | | | | | | 4Yr | Stanford University (Palo Alto, CA) |
| 2006 | 36 | | 1080 | FrRnd | 14 | Blue Jays | Dominique Rodgers (minors) | | | | | | | | | | | | | JC | Sacramento City College (Sacramento, CA) |
| 2006 | 36 | | 1085 | FrRnd | 19 | Marlins | David Williams (minors) | | | | | | | | | | | | | 4Yr | Rutgers, the State University of New Jersey (New Brunswick, NJ) |
| 2006 | 36 | | 1086 | FrRnd | 20 | Twins | J.D. Martinez (minors) | -0.4 | 194 | 691 | 21 | .252 | .711 | | | | | | | HS | Charles Flanagan HS (Pembroke Pines, FL) |
| 2006 | 36 | | 1090 | FrRnd | 24 | Braves | Sampson Williams (minors) | | | | | | | | | | | | | HS | Emsley A. Laney HS (Wilmington, NC) |
| 2006 | 37 | | 1100 | FrRnd | 4 | Pirates | Damian Walcott (minors) | | | | | | | | | | | | | JC | Brookdale Community College (Lincroft, NJ) |
| 2006 | 37 | | 1104 | FrRnd | 8 | Reds | Jarrod Gaskey (minors) | | | | | | | | | | | | | HS | Azle HS (Azle, TX) |
| 2006 | 37 | | 1105 | FrRnd | 9 | Orioles | Michael Lane (minors) | | | | | | | | | | | | | HS | Daviess County HS (Owensboro, KY) |
| 2006 | 37 | | 1106 | FrRnd | 10 | Giants | Lance Salsgiver (minors) | | | | | | | | | | | | | 4Yr | Harvard University (Cambridge, MA) |
| 2006 | 37 | | 1110 | FrRnd | 14 | Blue Jays | Benjamin Zeskind (minors) | | | | | | | | | | | | | 4Yr | University of Richmond (Richmond, VA) |
| 2006 | 37 | | 1118 | FrRnd | 22 | Athletics | David Fry (minors) | | | | | | | | | | | | | HS | Bishop Gorman HS (Las Vegas, NV) |
| 2006 | 37 | | 1122 | FrRnd | 26 | Angels | Ronnie Welty (minors) | | | | | | | | | | | | | HS | Mesquite HS (Gilbert, AZ) |
| 2006 | 37 | | 1125 | FrRnd | 29 | White Sox | Adan Severino (minors) | | | | | | | | | | | | | JC | Broward Community College (Fort Lauderdale, FL) |
| 2006 | 38 | | 1127 | FrRnd | 1 | Royals | Michael Dabbs (minors) | | | | | | | | | | | | | JC | Cowley County Community College (Arkansas City, KS) |
| 2006 | 38 | | 1131 | FrRnd | 5 | Mariners | Michael Drake (minors) | | | | | | | | | | | | | JC | Cosumnes River College (Sacramento, CA) |
| 2006 | 38 | | 1137 | FrRnd | 11 | Diamondbacks | Michael Guerrero (minors) | | | | | | | | | | | | | JC | Meridian Community College (Meridian, MS) |
| 2006 | 38 | | 1139 | FrRnd | 13 | Cubs | Benjamin Feltner (minors) | | | | | | | | | | | | | JC | Temple College (Temple, TX) |
| 2006 | 38 | | 1150 | FrRnd | 24 | Braves | Joshua Ashton (minors) | | | | | | | | | | | | | HS | Rose HS (Greenville, NC) |
| 2006 | 38 | | 1154 | FrRnd | 28 | Yankees | Nicholas Diyorio (minors) | | | | | | | | | | | | | 4Yr | Florida Southern College (Lakeland, FL) |
| 2006 | 39 | | 1159 | FrRnd | 3 | Devil Rays | Matt Miraldi (minors) | | | | | | | | | | | | | HS | Bear River HS (Grass Valley, CA) |
| 2006 | 39 | | 1160 | FrRnd | 4 | Pirates | Tom Hagan (minors) | | | | | | | | | | | | | 4Yr | University of Virginia (Charlottesville, VA) |
| 2006 | 39 | | 1167 | FrRnd | 11 | Diamondbacks | Riley Etchebarren (minors) | | | | | | | | | | | | | HS | Paradise Valley HS (Phoenix, AZ) |
| 2006 | 39 | | 1169 | FrRnd | 13 | Cubs | Marcus Hatley (minors) | | | | | | | | | | | | | HS | Mission Hills HS (Mission Hills, CA) |
| 2006 | 39 | | 1172 | FrRnd | 16 | Brewers | Chuckie Caufield (minors) | | | | | | | | | | | | | 4Yr | University of Oklahoma (Norman, OK) |
| 2006 | 39 | | 1174 | FrRnd | 18 | Mets | Donald Green (minors) | | | | | | | | | | | | | 4Yr | Texas Southern University (Houston, TX) |
| 2006 | 39 | | 1175 | FrRnd | 19 | Marlins | Spike McDougall (minors) | | | | | | | | | | | | | 4Yr | University of California, Irvine (Irvine, CA) |
| 2006 | 39 | | 1182 | FrRnd | 26 | Angels | Rian Kiniry (minors) | | | | | | | | | | | | | JC | Broward Community College (Fort Lauderdale, FL) |
| 2006 | 40 | | 1194 | FrRnd | 8 | Reds | Tyler Dewitt (minors) | | | | | | | | | | | | | HS | Ponderosa HS (Shingle Springs, CA) |
| 2006 | 40 | | 1196 | FrRnd | 10 | Giants | Jonathon Amaya (minors) | | | | | | | | | | | | | HS | Diamond Bar HS (Diamond Bar, CA) |
| 2006 | 40 | | 1210 | FrRnd | 24 | Braves | Tyreace House (minors) | | | | | | | | | | | | | HS | Palmdale HS (Palmdale, CA) |
| 2006 | 40 | | 1215 | FrRnd | 29 | White Sox | Andrew Mead (minors) | | | | | | | | | | | | | 4Yr | State University of New York at Cortland (Cortland, NY) |
| 2006 | 41 | | 1219 | FrRnd | 3 | Devil Rays | Mike Dufek (minors) | | | | | | | | | | | | | HS | Desert Mountain HS (Scottsdale, AZ) |
| 2006 | 41 | | 1239 | FrRnd | 23 | Astros | Axel Gonzalez (minors) | | | | | | | | | | | | | HS | Rosalina C. Martinez School (Guaynabo, PR) |
| 2006 | 41 | | 1242 | FrRnd | 26 | Angels | Brian Hobbs (minors) | | | | | | | | | | | | | JC | Chipola College (Marianna, FL) |
| 2006 | 41 | | 1244 | FrRnd | 28 | Yankees | Ohmed Danesh (minors) | | | | | | | | | | | | | HS | Dr. Phillips HS (Orlando, FL) |
| 2006 | 42 | | 1247 | FrRnd | 1 | Royals | Todd McBride (minors) | | | | | | | | | | | | | HS | The Dalles HS (The Dalles, OR) |
| 2006 | 42 | | 1253 | FrRnd | 7 | Dodgers | Joe Dispensa (minors) | | | | | | | | | | | | | HS | St. Rita HS (Chicago, IL) |
| 2006 | 42 | | 1258 | FrRnd | 12 | Rangers | Lance West (minors) | | | | | | | | | | | | | HS | Captain Shreve HS (Shreveport, LA) |
| 2006 | 42 | | 1259 | FrRnd | 13 | Cubs | Benjamin Ornelas (minors) | | | | | | | | | | | | | JC | Cypress College (Cypress, CA) |
| 2006 | 42 | | 1270 | FrRnd | 24 | Indians | Roderick Barcelo (minors) | | | | | | | | | | | | | HS | Lind Padron Rivera HS (Vega Baja, PR) |
| 2006 | 43 | | 1277 | FrRnd | 2 | Rockies | Bryan Jaeger (minors) | | | | | | | | | | | | | JC | Louisiana State University, Eunice (Eunice, LA) |
| 2006 | 43 | | 1278 | FrRnd | 3 | Devil Rays | Victor Ramos (minors) | | | | | | | | | | | | | HS | Miami Senior HS (Miami, FL) |
| 2006 | 43 | | 1284 | FrRnd | 9 | Orioles | Jose Kianes (minors) | | | | | | | | | | | | | HS | Martin County HS (Stuart, FL) |
| 2006 | 43 | | 1297 | FrRnd | 22 | Astros | Greg Joseph (minors) | | | | | | | | | | | | | JC | Mount San Antonio College (Walnut, CA) |
| 2006 | 43 | | 1298 | FrRnd | 23 | Braves | L.V. Ware (minors) | | | | | | | | | | | | | JC | Okaloosa-Walton College (Niceville, FL) |
| 2006 | 43 | | 1301 | FrRnd | 26 | Red Sox | Jeff Vincent (minors) | | | | | | | | | | | | | 4Yr | Niagara University (Lewiston, NY) |
| 2006 | 43 | | 1303 | FrRnd | 28 | White Sox | Jordan Cheatham (minors) | | | | | | | | | | | | | HS | Pike HS (Indianapolis, IN) |
| 2006 | 44 | | 1307 | FrRnd | 3 | Devil Rays | Neil Hardon (minors) | | | | | | | | | | | | | HS | Saguaro HS (Scottsdale, AZ) |
| 2006 | 44 | | 1310 | FrRnd | 6 | Tigers | Ryan Kilmer (minors) | | | | | | | | | | | | | HS | Midwest City HS (Midwest City, OK) |
| 2006 | 44 | | 1312 | FrRnd | 8 | Reds | Jason Chapman (minors) | | | | | | | | | | | | | HS | Truckee HS (Truckee, CA) |
| 2006 | 44 | | 1325 | FrRnd | 21 | Phillies | Mike Petello (minors) | | | | | | | | | | | | | HS | Saguaro HS (Scottsdale, AZ) |
| 2006 | 44 | | 1326 | FrRnd | 22 | Astros | Adam Pilate (minors) | | | | | | | | | | | | | HS | Sylacauga HS (Sylacauga, AL) |
| 2006 | 44 | | 1333 | FrRnd | 29 | Cardinals | Cameron Grant (minors) | | | | | | | | | | | | | HS | Hermitage HS (Hermitage, VA) |
| 2006 | 45 | | 1339 | FrRnd | 6 | Tigers | Lance Durham (minors) | | | | | | | | | | | | | HS | Roger Bacon HS (St. Bernard, OH) |
| 2006 | 45 | | 1342 | FrRnd | 9 | Orioles | Isaiah Stanback (minors) | | | | | | | | | | | | | 4Yr | University of Washington (Seattle, WA) |
| 2006 | 45 | | 1346 | FrRnd | 13 | Cubs | Elliot Shea (minors) | | | | | | | | | | | | | 4Yr | Franklin Pierce University (Rindge, NH) |
| 2006 | 45 | | 1355 | FrRnd | 22 | Astros | Cody Madison (minors) | | | | | | | | | | | | | HS | Vista Del Lago HS (Folsom, CA) |
| 2006 | 45 | | 1357 | FrRnd | 24 | Indians | Zachariah Barger (minors) | | | | | | | | | | | | | JC | Grossmont College (El Cajon, CA) |
| 2006 | 45 | | 1361 | FrRnd | 28 | White Sox | Raul Duran (minors) | | | | | | | | | | | | | HS | Saddleback HS (Santa Ana, CA) |
| 2006 | 46 | | 1364 | FrRnd | 2 | Rockies | Damion Carter (minors) | | | | | | | | | | | | | 4Yr | University of Southern Mississippi (Hattiesburg, MS) |
| 2006 | 46 | | 1365 | FrRnd | 3 | Devil Rays | Candy Maldonado (minors) | | | | | | | | | | | | | JC | Porterville JC (Porterville, CA) |
| 2006 | 46 | | 1366 | FrRnd | 4 | Pirates | Ryan Groth (minors) | | | | | | | | | | | | | JC | Indian River Community College (Fort Pierce, FL) |
| 2006 | 46 | | 1374 | FrRnd | 12 | Rangers | Clifton Thomas (minors) | | | | | | | | | | | | | HS | El Cajon Valley HS (El Cajon, CA) |
| 2006 | 46 | | 1381 | FrRnd | 19 | Twins | Richard Breton (minors) | | | | | | | | | | | | | HS | Keystone HS (Keystone, FL) |
| 2006 | 47 | | 1395 | FrRnd | 5 | Mariners | Sean Ward (minors) | | | | | | | | | | | | | HS | Evans HS (Martinez, GA) |
| 2006 | 47 | | 1409 | FrRnd | 19 | Twins | Joshua Chester (minors) | | | | | | | | | | | | | HS | Cypress Bay HS (Cypress Bay, FL) |
| 2006 | 47 | | 1413 | FrRnd | 23 | Indians | Eric McKinney (minors) | | | | | | | | | | | | | HS | Spiro HS (Spiro, OK) |
| 2006 | 48 | | 1433 | FrRnd | 15 | Nationals | Kyle Page (minors) | | | | | | | | | | | | | JC | Brevard Community College (Cocoa, FL) |
| 2006 | 49 | | 1452 | FrRnd | 6 | Tigers | Kyle Peter (minors) | | | | | | | | | | | | | JC | Cloud County CC (Concordia, KS) |
| 2006 | 49 | | 1454 | FrRnd | 8 | Reds | Cameron Bayne (minors) | | | | | | | | | | | | | HS | St. Louis HS (Honolulu, HI) |
| 2006 | 49 | | 1458 | FrRnd | 12 | Rangers | James Stubbs (minors) | | | | | | | | | | | | | HS | Atlanta HS (Atlanta, TX) |
| 2006 | 49 | | 1464 | FrRnd | 18 | Marlins | Michael Hubbard (minors) | | | | | | | | | | | | | 4Yr | University of Arkansas-Fort Smith (Fort Smith, AR) |
| 2006 | 49 | | 1465 | FrRnd | 19 | Twins | Calvin Culver (minors) | | | | | | | | | | | | | HS | Quartz Hill HS (Quartz Hill, CA) |
| 2006 | 49 | | 1468 | FrRnd | 22 | Braves | Blake Holt (minors) | | | | | | | | | | | | | JC | Temple College (Temple, TX) |
| 2006 | 49 | | 1472 | FrRnd | 26 | Yankees | Chase Odenreider (minors) | | | | | | | | | | | | | 4Yr | Creighton University (Omaha, NE) |
| 2006 | 49 | | 1474 | FrRnd | 28 | Cardinals | Gary Taylor (minors) | | | | | | | | | | | | | JC | Holmes Community College (Ridgeland, MS) |
| 2006 | 50 | | 1475 | FrRnd | 1 | Royals | Jarrod Dyson (minors) | 3.2 | 164 | 434 | 2 | .249 | .662 | | | | | | | JC | Southwest JC (Summit, MS) |
| 2006 | 50 | | 1476 | FrRnd | 2 | Rockies | Jamie Johnson (minors) | | | | | | | | | | | | | HS | West Ouacita HS (West Monroe, LA) |
| 2006 | 50 | | 1478 | FrRnd | 4 | Pirates | Marquise Zachery (minors) | | | | | | | | | | | | | JC | Florida Gateway College (Lake City, FL) |
| 2006 | 50 | | 1480 | FrRnd | 6 | Tigers | Alan Oaks (minors) | | | | | | | | | | | | | HS | Divine Child HS (Dearborn, MI) |
| 2006 | 50 | | 1488 | FrRnd | 14 | Blue Jays | Baron Frost (minors) | | | | | | | | | | | | | 4Yr | University of Southern California (Los Angeles, CA) |
| 2006 | 50 | | 1495 | FrRnd | 21 | Astros | Tyler Henley (minors) | | | | | | | | | | | | | 4Yr | Rice University (Houston, TX) |
| 2006 | 50 | | 1501 | FrRnd | 27 | White Sox | Brendon O'Donnell (minors) | | | | | | | | | | | | | 4Yr | University of Texas of the Permian Basin (Odessa, TX) |