| 2006 | 1 | | 6 | FrRnd | 6 | Tigers | Andrew Miller (minors) | -2.9 | 171 | 72 | 0 | .056 | .111 | 171 | 24 | 32 | 5.47 | 1.68 | 0 | 4Yr | University of North Carolina at Chapel Hill (Chapel Hill, NC) |
| 2006 | 1 | | 7 | FrRnd | 7 | Dodgers | Clayton Kershaw (minors) | 28.3 | 163 | 284 | 1 | .148 | .347 | 161 | 66 | 39 | 2.69 | 1.11 | 0 | HS | Highland Park HS (Highland Park, TX) |
| 2006 | 1 | | 12 | FrRnd | 12 | Rangers | Kasey Kiker (minors) | | | | | | | | | | | | | HS | Russell County HS (Seale, AL) |
| 2006 | 1s | | 39 | FrRnd | 39 | Indians | *David Huff (minors) | -1.6 | 58 | 4 | 0 | .000 | .000 | 58 | 18 | 26 | 5.40 | 1.56 | 0 | 4Yr | University of California, Los Angeles (Los Angeles, CA) |
| 2006 | 1s | | 40 | FrRnd | 40 | Red Sox | *Kris Johnson (minors) | | | | | | | | | | | | | 4Yr | Wichita State University (Wichita, KS) |
| 2006 | 1s | | 43 | FrRnd | 43 | Braves | *Steve Evarts (minors) | | | | | | | | | | | | | HS | T. R. Robinson HS (Tampa, FL) |
| 2006 | 2 | | 48 | FrRnd | 4 | Pirates | Michael Felix (minors) | | | | | | | | | | | | | 4Yr | Troy University (Troy, AL) |
| 2006 | 2 | | 51 | FrRnd | 7 | Braves via Dodgers | *Jeff Locke (minors) | -0.1 | 21 | 30 | 0 | .033 | .098 | 21 | 5 | 7 | 4.25 | 1.34 | 0 | HS | A. Crosby Kennett HS (Conway, NH) |
| 2006 | 2 | | 54 | FrRnd | 10 | Cardinals via Giants | *Brad Furnish (minors) | | | | | | | | | | | | | 4Yr | Texas Christian University (Fort Worth, TX) |
| 2006 | 2 | | 55 | FrRnd | 11 | Diamondbacks | Brett Anderson (minors) | 5.8 | 74 | 4 | 0 | .000 | .000 | 74 | 26 | 29 | 3.74 | 1.27 | 0 | HS | Stillwater HS (Stillwater, OK) |
| 2006 | 2 | | 61 | FrRnd | 17 | Padres | Wade LeBlanc (minors) | 1.7 | 91 | 111 | 0 | .252 | .540 | 90 | 19 | 32 | 4.52 | 1.44 | 0 | 4Yr | University of Alabama (Tuscaloosa, AL) |
| 2006 | 3 | | 78 | FrRnd | 2 | Rockies | Keith Weiser (minors) | | | | | | | | | | | | | 4Yr | Miami University of Ohio (Oxford, OH) |
| 2006 | 3 | | 81 | FrRnd | 5 | Mariners | Tony Butler (minors) | | | | | | | | | | | | | HS | Oak Creek HS (Oak Creek, WI) |
| 2006 | 3 | | 85 | FrRnd | 9 | Orioles | Zach Britton (minors) | 0.7 | 41 | 8 | 1 | .625 | 1.750 | 41 | 16 | 15 | 4.85 | 1.49 | 0 | HS | Weatherford HS (Weatherford, TX) |
| 2006 | 3 | | 89 | FrRnd | 13 | Giants via Cubs | *Clayton Tanner (minors) | | | | | | | | | | | | | HS | De La Salle HS (Concord, CA) |
| 2006 | 3 | | 96 | FrRnd | 20 | Twins | Tyler Robertson (minors) | -0.5 | 42 | 0 | 0 | | | 42 | 2 | 2 | 5.54 | 1.38 | 0 | HS | Bella Vista HS (Fair Oaks, CA) |
| 2006 | 3 | | 100 | FrRnd | 24 | Braves | Chad Rodgers (minors) | | | | | | | | | | | | | HS | Walsh Jesuit HS (Cuyahoga Falls, OH) |
| 2006 | 3 | | 105 | FrRnd | 29 | White Sox | Justin Edwards (minors) | | | | | | | | | | | | | HS | Olympia HS (Orlando, FL) |
| 2006 | 4 | | 116 | FrRnd | 10 | Giants | Ben Snyder (minors) | | | | | | | | | | | | | 4Yr | Ball State University (Muncie, IN) |
| 2006 | 4 | | 121 | FrRnd | 15 | Nationals | Glenn Gibson (minors) | | | | | | | | | | | | | HS | Center Moriches HS (Center Moriches, NY) |
| 2006 | 4 | | 123 | FrRnd | 17 | Padres | Nathan Culp (minors) | | | | | | | | | | | | | 4Yr | University of Missouri Columbia (Columbia, MO) |
| 2006 | 4 | | 130 | FrRnd | 24 | Braves | Lee Hyde (minors) | | | | | | | | | | | | | 4Yr | Georgia Institute of Technology (Atlanta, GA) |
| 2006 | 4 | | 131 | FrRnd | 25 | Indians | Ryan Morris (minors) | | | | | | | | | | | | | HS | South Mecklenburg HS (Charlotte, NC) |
| 2006 | 5 | | 151 | FrRnd | 15 | Nationals | Cory VanAllen (minors) | | | | | | | | | | | | | 4Yr | Baylor University (Waco, TX) |
| 2006 | 5 | | 160 | FrRnd | 24 | Braves | Kevin Gunderson (minors) | | | | | | | | | | | | | 4Yr | Oregon State University (Corvallis, OR) |
| 2006 | 5 | | 163 | FrRnd | 27 | Red Sox | Dustin Richardson (minors) | 0.4 | 29 | 0 | 0 | | | 29 | 0 | 0 | 3.31 | 2.02 | 0 | 4Yr | Texas Tech University (Lubbock, TX) |
| 2006 | 6 | | 173 | FrRnd | 7 | Dodgers | Garrett White (minors) | | | | | | | | | | | | | 4Yr | University of Mississippi (Oxford, MS) |
| 2006 | 6 | | 182 | FrRnd | 16 | Brewers | Brae Wright (minors) | | | | | | | | | | | | | 4Yr | Oklahoma State University (Stillwater, OK) |
| 2006 | 6 | | 187 | FrRnd | 21 | Phillies | Daniel Brauer (minors) | | | | | | | | | | | | | 4Yr | Northwestern University (Evanston, IL) |
| 2006 | 6 | | 192 | FrRnd | 26 | Angels | Robert Fish (minors) | | | | | | | | | | | | | HS | A. B. Miller HS (Fontana, CA) |
| 2006 | 6 | | 196 | FrRnd | 30 | Cardinals | Tyler Norrick (minors) | | | | | | | | | | | | | 4Yr | Southern Illinois University Carbondale (Carbondale, IL) |
| 2006 | 7 | | 219 | FrRnd | 23 | Astros | David Qualben (minors) | | | | | | | | | | | | | 4Yr | Pace University (New York, NY) |
| 2006 | 8 | | 232 | FrRnd | 6 | Tigers | Chris Cody (minors) | | | | | | | | | | | | | 4Yr | Manhattan College (New York, NY) |
| 2006 | 8 | | 234 | FrRnd | 8 | Reds | Travis Webb (minors) | | | | | | | | | | | | | 4Yr | Washington State University (Pullman, WA) |
| 2006 | 8 | | 240 | FrRnd | 14 | Blue Jays | Danny O'Brien (minors) | | | | | | | | | | | | | 4Yr | Western Michigan University (Kalamazoo, MI) |
| 2006 | 9 | | 262 | FrRnd | 6 | Tigers | Zach Piccola (minors) | | | | | | | | | | | | | 4Yr | University of South Alabama (Mobile, AL) |
| 2006 | 9 | | 265 | FrRnd | 9 | Orioles | Brett Bordes (minors) | | | | | | | | | | | | | 4Yr | Arizona State University (Tempe, AZ) |
| 2006 | 9 | | 267 | FrRnd | 11 | Diamondbacks | Eddie Romero (minors) | | | | | | | | | | | | | 4Yr | California State University Fresno (Fresno, CA) |
| 2006 | 9 | | 271 | FrRnd | 15 | Nationals | Joey Rosas (minors) | | | | | | | | | | | | | JC | Yavapai College (Prescott, AZ) |
| 2006 | 9 | | 276 | FrRnd | 20 | Twins | Sean Land (minors) | | | | | | | | | | | | | 4Yr | University of Kansas (Lawrence, KS) |
| 2006 | 9 | | 282 | FrRnd | 26 | Angels | Nate Boman (minors) | | | | | | | | | | | | | 4Yr | University of San Diego (San Diego, CA) |
| 2006 | 10 | | 290 | FrRnd | 4 | Pirates | Charles Benoit (minors) | | | | | | | | | | | | | 4Yr | Oklahoma State University (Stillwater, OK) |
| 2006 | 10 | | 296 | FrRnd | 10 | Giants | Ryan Paul (minors) | | | | | | | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 2006 | 10 | | 305 | FrRnd | 19 | Marlins | Graham Taylor (minors) | -0.6 | 3 | 3 | 0 | .000 | .000 | 3 | 0 | 2 | 8.18 | 2.55 | 0 | 4Yr | Miami University of Ohio (Oxford, OH) |
| 2006 | 10 | | 312 | FrRnd | 26 | Angels | Leo Calderon (minors) | | | | | | | | | | | | | JC | Florida Gateway College (Lake City, FL) |
| 2006 | 11 | | 339 | FrRnd | 23 | Astros | Tom Vessella (minors) | | | | | | | | | | | | | 4Yr | Whittier College (Whittier, CA) |
| 2006 | 12 | | 347 | FrRnd | 1 | Royals | Everett Teaford (minors) | 0.8 | 44 | 0 | 0 | | | 44 | 3 | 5 | 4.27 | 1.32 | 1 | 4Yr | Georgia Southern University (Statesboro, GA) |
| 2006 | 12 | | 353 | FrRnd | 7 | Dodgers | Paul Coleman (minors) | | | | | | | | | | | | | 4Yr | Pepperdine University (Malibu, CA) |
| 2006 | 13 | | 379 | FrRnd | 3 | Devil Rays | Mike Minor (minors) | 1.5 | 63 | 108 | 0 | .074 | .225 | 63 | 24 | 17 | 4.11 | 1.25 | 0 | HS | Forrest HS (Forrest, TN) |
| 2006 | 13 | | 388 | FrRnd | 12 | Rangers | Kevin Angelle (minors) | | | | | | | | | | | | | HS | Bridge City HS (Bridge City, TX) |
| 2006 | 13 | | 398 | FrRnd | 22 | Athletics | Ben Jukich (minors) | | | | | | | | | | | | | 4Yr | Dakota Wesleyan University (Mitchell, SD) |
| 2006 | 13 | | 399 | FrRnd | 23 | Astros | Chris Salamida (minors) | | | | | | | | | | | | | 4Yr | State University of New York at Oneonta (Oneonta, NY) |
| 2006 | 13 | | 402 | FrRnd | 26 | Angels | Blake Holler (minors) | | | | | | | | | | | | | 4Yr | Stanford University (Palo Alto, CA) |
| 2006 | 14 | | 418 | FrRnd | 12 | Rangers | Mike Ballard (minors) | | | | | | | | | | | | | 4Yr | University of Virginia (Charlottesville, VA) |
| 2006 | 14 | | 424 | FrRnd | 18 | Mets | Todd Privett (minors) | | | | | | | | | | | | | JC | College of Southern Idaho (Twin Falls, ID) |
| 2006 | 14 | | 431 | FrRnd | 25 | Indians | William Delage (minors) | | | | | | | | | | | | | 4Yr | Lamar University (Beaumont, TX) |
| 2006 | 14 | | 432 | FrRnd | 26 | Angels | Chris Armstrong (minors) | | | | | | | | | | | | | HS | Owasso HS (Owasso, OK) |
| 2006 | 15 | | 446 | FrRnd | 10 | Giants | Andrew Barbosa (minors) | | | | | | | | | | | | | HS | Riverview HS (Riverview, FL) |
| 2006 | 15 | | 459 | FrRnd | 23 | Astros | Kevin Fox (minors) | | | | | | | | | | | | | 4Yr | Biola University (La Mirada, CA) |
| 2006 | 15 | | 461 | FrRnd | 25 | Indians | Matt Meyer (minors) | | | | | | | | | | | | | 4Yr | Boston College (Chestnut Hill, MA) |
| 2006 | 16 | | 469 | FrRnd | 3 | Devil Rays | Ryan Owen (minors) | | | | | | | | | | | | | 4Yr | California State University Dominguez Hills (Carson, CA) |
| 2006 | 16 | | 474 | FrRnd | 8 | Reds | Jamie Arneson (minors) | | | | | | | | | | | | | JC | Bakersfield College (Bakersfield, CA) |
| 2006 | 16 | | 476 | FrRnd | 10 | Giants | Paul Oseguera (minors) | | | | | | | | | | | | | 4Yr | University of California, Los Angeles (Los Angeles, CA) |
| 2006 | 16 | | 488 | FrRnd | 22 | Athletics | Branden Dewing (minors) | | | | | | | | | | | | | 4Yr | San Jose State University (San Jose, CA) |
| 2006 | 17 | | 501 | FrRnd | 5 | Mariners | Dan Runzler (minors) | 0.3 | 89 | 1 | 0 | .000 | .500 | 89 | 4 | 2 | 3.86 | 1.51 | 0 | 4Yr | University of California, Riverside (Riverside, CA) |
| 2006 | 17 | | 505 | FrRnd | 9 | Orioles | Tony Watson (minors) | 0.5 | 131 | 2 | 0 | .000 | .000 | 131 | 8 | 5 | 3.88 | 1.21 | 1 | 4Yr | University of Nebraska at Lincoln (Lincoln, NE) |
| 2006 | 17 | | 516 | FrRnd | 20 | Twins | Andy Oliver (minors) | -0.8 | 7 | 2 | 0 | .000 | .000 | 7 | 0 | 5 | 7.11 | 1.83 | 0 | HS | Vermilion HS (Vermilion, OH) |
| 2006 | 17 | | 520 | FrRnd | 24 | Braves | Clayton McMillan (minors) | | | | | | | | | | | | | JC | Texarkana College (Texarkana, TX) |
| 2006 | 18 | | 535 | FrRnd | 9 | Orioles | Nathan Nery (minors) | | | | | | | | | | | | | 4Yr | Stetson University (DeLand, FL) |
| 2006 | 18 | | 540 | FrRnd | 14 | Blue Jays | Kyle Walter (minors) | | | | | | | | | | | | | 4Yr | Bucknell University (Lewisburg, PA) |
| 2006 | 18 | | 546 | FrRnd | 20 | Twins | Chris Anderson (minors) | | | | | | | | | | | | | JC | Northern Essex Community College (Haverhill, MA) |
| 2006 | 18 | | 554 | FrRnd | 28 | Yankees | Del Howell (minors) | | | | | | | | | | | | | HS | American Christian Academy (Tuscaloosa, AL) |
| 2006 | 18 | | 555 | FrRnd | 29 | White Sox | Lucas Luetge (minors) | -0.2 | 73 | 0 | 0 | | | 73 | 2 | 3 | 4.80 | 1.58 | 2 | JC | San Jacinto College (Pasadena, TX) |
| 2006 | 19 | | 562 | FrRnd | 6 | Tigers | Duane Below (minors) | -0.0 | 42 | 1 | 0 | .000 | .000 | 42 | 2 | 4 | 4.36 | 1.32 | 0 | JC | Lake Michigan CC (Benton Harbor, MI) |
| 2006 | 19 | | 569 | FrRnd | 13 | Cubs | Jeremy Papelbon (minors) | | | | | | | | | | | | | 4Yr | University of North Florida (Jacksonville, FL) |
| 2006 | 19 | | 574 | FrRnd | 18 | Mets | Justin Woodall (minors) | | | | | | | | | | | | | HS | Lafayette HS (Lafayette, MS) |
| 2006 | 20 | | 602 | FrRnd | 16 | Brewers | Mehdi Djebbar (minors) | | | | | | | | | | | | | JC | Ahuntsic College (Cap-Rouge, QC) |
| 2006 | 20 | | 607 | FrRnd | 21 | Phillies | Domonic Brown (minors) | -1.3 | 193 | 598 | 20 | .239 | .711 | | | | | | | HS | Redan HS (Stone Mountain, GA) |
| 2006 | 20 | | 612 | FrRnd | 26 | Angels | J.D. Reichenbach (minors) | | | | | | | | | | | | | HS | Central Bucks HS East (Doylestown, PA) |
| 2006 | 21 | | 617 | FrRnd | 1 | Royals | Burke Baldwin (minors) | | | | | | | | | | | | | JC | Elgin CC (Elgin, IL) |
| 2006 | 21 | | 621 | FrRnd | 5 | Mariners | Brent Gaphardt (minors) | | | | | | | | | | | | | 4Yr | University of Delaware (Newark, DE) |
| 2006 | 21 | | 622 | FrRnd | 6 | Tigers | Tom Thornton (minors) | | | | | | | | | | | | | 4Yr | University of Notre Dame (South Bend, IN) |
| 2006 | 21 | | 626 | FrRnd | 10 | Giants | Steven Calicutt (minors) | | | | | | | | | | | | | 4Yr | East Tennessee State University (Johnson City, TN) |
| 2006 | 21 | | 629 | FrRnd | 13 | Cubs | Taylor Parker (minors) | | | | | | | | | | | | | 4Yr | University of Missouri Columbia (Columbia, MO) |
| 2006 | 21 | | 630 | FrRnd | 14 | Blue Jays | Ron Lowe (minors) | | | | | | | | | | | | | 4Yr | St. Leo College (St. Leo, FL) |
| 2006 | 21 | | 639 | FrRnd | 23 | Astros | Anthony Bello (minors) | | | | | | | | | | | | | 4Yr | Nova Southeastern University (Fort Lauderdale, FL) |
| 2006 | 21 | | 641 | FrRnd | 25 | Indians | John Gaub (minors) | -0.1 | 4 | 0 | 0 | | | 4 | 0 | 0 | 6.75 | 1.50 | 0 | 4Yr | University of Minnesota (Minneapolis, MN) |
| 2006 | 22 | | 651 | FrRnd | 5 | Mariners | Fabian Williamson (minors) | | | | | | | | | | | | | HS | Kennedy HS (Granada Hills, CA) |
| 2006 | 22 | | 655 | FrRnd | 9 | Orioles | Chris Salberg (minors) | | | | | | | | | | | | | 4Yr | Florida Atlantic University (Boca Raton, FL) |
| 2006 | 22 | | 658 | FrRnd | 12 | Rangers | Cory Luebke (minors) | 2.4 | 56 | 49 | 0 | .143 | .319 | 55 | 10 | 12 | 3.25 | 1.10 | 0 | 4Yr | The Ohio State University (Columbus, OH) |
| 2006 | 22 | | 660 | FrRnd | 14 | Blue Jays | Brad Mills (minors) | -1.0 | 15 | 1 | 0 | .000 | .000 | 15 | 3 | 3 | 7.76 | 1.71 | 0 | 4Yr | University of Arizona (Tucson, AZ) |
| 2006 | 22 | | 665 | FrRnd | 19 | Marlins | Kevan Kelley (minors) | | | | | | | | | | | | | 4Yr | California State University San Bernardino (San Bernardino, CA) |
| 2006 | 22 | | 666 | FrRnd | 20 | Twins | Aaron Tennyson (minors) | | | | | | | | | | | | | 4Yr | University of Kentucky (Lexington, KY) |
| 2006 | 22 | | 670 | FrRnd | 24 | Braves | Cole Rohrbough (minors) | | | | | | | | | | | | | JC | Western Nevada College (Carson City, NV) |
| 2006 | 23 | | 678 | FrRnd | 2 | Rockies | Scott Maine (minors) | -0.4 | 50 | 2 | 0 | .000 | .000 | 50 | 2 | 3 | 5.59 | 1.61 | 0 | 4Yr | University of Miami (Coral Gables, FL) |
| 2006 | 23 | | 682 | FrRnd | 6 | Tigers | Aaron Fuhrman (minors) | | | | | | | | | | | | | HS | Pleasant Valley HS (Pleasant Valley, PA) |
| 2006 | 23 | | 691 | FrRnd | 15 | Nationals | Forrest Beverly (minors) | | | | | | | | | | | | | 4Yr | University of South Carolina (Columbia, SC) |
| 2006 | 23 | | 693 | FrRnd | 17 | Padres | Brooks Dunn (minors) | | | | | | | | | | | | | 4Yr | Mississippi State University (Mississippi State, MS) |
| 2006 | 23 | | 695 | FrRnd | 19 | Marlins | Rylan Hanks (minors) | | | | | | | | | | | | | 4Yr | California State University San Bernardino (San Bernardino, CA) |
| 2006 | 23 | | 701 | FrRnd | 25 | Indians | Derrick Loop (minors) | | | | | | | | | | | | | 4Yr | California State University Los Angeles (Los Angeles, CA) |
| 2006 | 23 | | 704 | FrRnd | 28 | Yankees | Brandon Thomson (minors) | | | | | | | | | | | | | JC | Chandler-Gilbert Community College (Chandler, AZ) |
| 2006 | 23 | | 705 | FrRnd | 29 | White Sox | Brandon Villalobos (minors) | | | | | | | | | | | | | JC | Chaffey College (Rancho Cucamonga, CA) |
| 2006 | 24 | | 718 | FrRnd | 12 | Rangers | Lance McClain (minors) | | | | | | | | | | | | | JC | Walters State Community College (Morristown, TN) |
| 2006 | 24 | | 729 | FrRnd | 23 | Astros | John Wiedenbauer (minors) | | | | | | | | | | | | | HS | Seabreeze HS (Daytona Beach, FL) |
| 2006 | 24 | | 730 | FrRnd | 24 | Braves | Zac Oliver (minors) | | | | | | | | | | | | | JC | Paris Junior College (Paris, TX) |
| 2006 | 24 | | 736 | FrRnd | 30 | Cardinals | Roberto Gomez (minors) | | | | | | | | | | | | | 4Yr | University of Texas Pan American (Edinburg, TX) |
| 2006 | 25 | | 748 | FrRnd | 12 | Rangers | Derek Holland (minors) | 5.6 | 117 | 10 | 0 | .000 | .091 | 117 | 42 | 31 | 4.58 | 1.33 | 0 | JC | Wallace State Community College (Hanceville) (Hanceville, AL) |
| 2006 | 25 | | 751 | FrRnd | 15 | Nationals | James Birmingham (minors) | | | | | | | | | | | | | HS | Overbrook Senior HS (Pine Hill, NJ) |
| 2006 | 25 | | 758 | FrRnd | 22 | Athletics | Aaron Odom (minors) | | | | | | | | | | | | | 4Yr | Texas Tech University (Lubbock, TX) |
| 2006 | 26 | | 768 | FrRnd | 2 | Rockies | Devin Collis (minors) | | | | | | | | | | | | | 4Yr | University of Arkansas (Fayetteville, AR) |
| 2006 | 26 | | 771 | FrRnd | 5 | Mariners | Greg Moviel (minors) | | | | | | | | | | | | | 4Yr | Vanderbilt University (Nashville, TN) |
| 2006 | 26 | | 782 | FrRnd | 16 | Brewers | Marc Lewis (minors) | | | | | | | | | | | | | 4Yr | Creighton University (Omaha, NE) |
| 2006 | 26 | | 785 | FrRnd | 19 | Marlins | Andy Jackson (minors) | | | | | | | | | | | | | 4Yr | University of Central Arkansas (Conway, AR) |
| 2006 | 26 | | 788 | FrRnd | 22 | Athletics | Derrick Gordon (minors) | | | | | | | | | | | | | 4Yr | Lamar University (Beaumont, TX) |
| 2006 | 26 | | 792 | FrRnd | 26 | Angels | Ryan Kelley (minors) | | | | | | | | | | | | | JC | Indian River Community College (Fort Pierce, FL) |
| 2006 | 26 | | 794 | FrRnd | 28 | Yankees | Tim Dennehy (minors) | | | | | | | | | | | | | JC | Chandler-Gilbert Community College (Chandler, AZ) |
| 2006 | 27 | | 811 | FrRnd | 15 | Nationals | Dan Pfau (minors) | | | | | | | | | | | | | 4Yr | George Washington University (Washington, DC) |
| 2006 | 27 | | 825 | FrRnd | 29 | White Sox | Tyler Herriage (minors) | | | | | | | | | | | | | HS | Marcus HS (Flower Mound, TX) |
| 2006 | 28 | | 828 | FrRnd | 2 | Rockies | Tommy Baumgardner (minors) | | | | | | | | | | | | | 4Yr | University of Mississippi (Oxford, MS) |
| 2006 | 28 | | 830 | FrRnd | 4 | Pirates | Rudy Owens (minors) | | | | | | | | | | | | | HS | Mesa HS (Mesa, AZ) |
| 2006 | 28 | | 838 | FrRnd | 12 | Rangers | Shaeffer Hall (minors) | | | | | | | | | | | | | HS | Lee's Summit HS (Lee's Summit, MO) |
| 2006 | 28 | | 841 | FrRnd | 15 | Nationals | Michael Robbins (minors) | | | | | | | | | | | | | JC | Meridian Community College (Meridian, MS) |
| 2006 | 28 | | 845 | FrRnd | 19 | Marlins | Kedrick Martin (minors) | | | | | | | | | | | | | JC | Meridian Community College (Meridian, MS) |
| 2006 | 28 | | 852 | FrRnd | 26 | Angels | Barret Browning (minors) | -0.1 | 22 | 1 | 0 | .000 | .000 | 22 | 1 | 3 | 5.12 | 1.29 | 0 | 4Yr | Florida State University (Tallahassee, FL) |
| 2006 | 28 | | 853 | FrRnd | 27 | Red Sox | Carmine Giardina (minors) | | | | | | | | | | | | | HS | Durant HS (Plant City, FL) |
| 2006 | 28 | | 854 | FrRnd | 28 | Yankees | Barrett Bruce (minors) | | | | | | | | | | | | | HS | Flower Mound HS (Flower Mound, TX) |
| 2006 | 29 | | 861 | FrRnd | 5 | Mariners | Gregory Nesbitt (minors) | | | | | | | | | | | | | 4Yr | James Madison University (Harrisonburg, VA) |
| 2006 | 29 | | 868 | FrRnd | 12 | Rangers | Daniel Hoben (minors) | | | | | | | | | | | | | JC | Chandler-Gilbert Community College (Chandler, AZ) |
| 2006 | 29 | | 872 | FrRnd | 16 | Brewers | David Newmann (minors) | | | | | | | | | | | | | 4Yr | Texas A&M University (College Station, TX) |
| 2006 | 29 | | 875 | FrRnd | 19 | Marlins | Jonathan Van Looy (minors) | | | | | | | | | | | | | HS | John Swett HS (Crockett, CA) |
| 2006 | 29 | | 885 | FrRnd | 29 | White Sox | Garrett Johnson (minors) | | | | | | | | | | | | | HS | Orme School (Mayer, AZ) |
| 2006 | 30 | | 893 | FrRnd | 7 | Dodgers | Alexander Burkard (minors) | | | | | | | | | | | | | HS | Milton HS (Milton, GA) |
| 2006 | 30 | | 894 | FrRnd | 8 | Reds | Lee Tabor (minors) | | | | | | | | | | | | | 4Yr | Francis Marion University (Florence, SC) |
| 2006 | 30 | | 895 | FrRnd | 9 | Orioles | Chris Cassidy (minors) | | | | | | | | | | | | | JC | Riverside Community College (Riverside, CA) |
| 2006 | 30 | | 897 | FrRnd | 11 | Diamondbacks | Clay Zavada (minors) | 0.7 | 49 | 0 | 0 | | | 49 | 3 | 3 | 3.35 | 1.35 | 0 | 4Yr | Southern Illinois University Edwardsville (Edwardsville, IL) |
| 2006 | 30 | | 906 | FrRnd | 20 | Twins | Michael Mopas (minors) | | | | | | | | | | | | | JC | Golden West College (Huntington Beach, CA) |
| 2006 | 30 | | 911 | FrRnd | 25 | Indians | Brett Carlin (minors) | | | | | | | | | | | | | JC | Fullerton College (Fullerton, CA) |
| 2006 | 30 | | 912 | FrRnd | 26 | Angels | Kevin Skogley (minors) | | | | | | | | | | | | | 4Yr | University of Nevada-Las Vegas (Las Vegas, NV) |
| 2006 | 30 | | 915 | FrRnd | 29 | White Sox | Hector Santiago (minors) | 2.6 | 56 | 3 | 0 | .000 | .000 | 56 | 5 | 4 | 2.99 | 1.24 | 4 | HS | Bloomfield Tech (Bloomfield, NJ) |
| 2006 | 31 | | 926 | FrRnd | 10 | Giants | Matthew McMurtry (minors) | | | | | | | | | | | | | 4Yr | Minnesota State University, Mankato (Mankato, MN) |
| 2006 | 31 | | 931 | FrRnd | 15 | Nationals | Zach Baldwin (minors) | | | | | | | | | | | | | 4Yr | West Virginia State University (Institute, WV) |
| 2006 | 31 | | 940 | FrRnd | 24 | Braves | Eric Barrett (minors) | | | | | | | | | | | | | JC | John A Logan College (Carterville, IL) |
| 2006 | 32 | | 956 | FrRnd | 10 | Giants | Matt Fairel (minors) | | | | | | | | | | | | | HS | Winter Haven HS (Winter Haven, FL) |
| 2006 | 32 | | 961 | FrRnd | 15 | Nationals | Joseph Welsh (minors) | | | | | | | | | | | | | 4Yr | University of Toledo (Toledo, OH) |
| 2006 | 32 | | 968 | FrRnd | 22 | Athletics | Nick Hernandez (minors) | | | | | | | | | | | | | HS | Hialeah HS (Hialeah, FL) |
| 2006 | 32 | | 974 | FrRnd | 28 | Yankees | Tommy Palica (minors) | | | | | | | | | | | | | JC | Golden West College (Huntington Beach, CA) |
| 2006 | 33 | | 1006 | FrRnd | 30 | Cardinals | Brian Schroeder (minors) | | | | | | | | | | | | | 4Yr | University of California, Los Angeles (Los Angeles, CA) |
| 2006 | 34 | | 1008 | FrRnd | 2 | Rockies | Jamie Niley (minors) | | | | | | | | | | | | | HS | Elk Grove HS (Elk Grove, CA) |
| 2006 | 34 | | 1016 | FrRnd | 10 | Giants | Jared Cranston (minors) | | | | | | | | | | | | | 4Yr | University of Nebraska at Lincoln (Lincoln, NE) |
| 2006 | 34 | | 1033 | FrRnd | 27 | Red Sox | Bryan Morgado (minors) | | | | | | | | | | | | | HS | Florida Christian School (Miami, FL) |
| 2006 | 35 | | 1042 | FrRnd | 6 | Tigers | Paul Hammond (minors) | | | | | | | | | | | | | 4Yr | University of Michigan (Ann Arbor, MI) |
| 2006 | 35 | | 1045 | FrRnd | 9 | Orioles | Matt Drummond (minors) | | | | | | | | | | | | | HS | Paso Robles HS (Paso Robles, CA) |
| 2006 | 35 | | 1050 | FrRnd | 14 | Blue Jays | John Zinnicker (minors) | | | | | | | | | | | | | 4Yr | St. Bonaventure University (St. Bonaventure, NY) |
| 2006 | 35 | | 1058 | FrRnd | 22 | Athletics | Carlos Hernandez (minors) | | | | | | | | | | | | | JC | West Valley College (Saratoga, CA) |
| 2006 | 35 | | 1061 | FrRnd | 25 | Indians | Alan Brech (minors) | | | | | | | | | | | | | 4Yr | Bowling Green State University (Bowling Green, OH) |
| 2006 | 36 | | 1069 | FrRnd | 3 | Devil Rays | Walter Marciel (minors) | | | | | | | | | | | | | HS | Iolani HS (Iolani, HI) |
| 2006 | 36 | | 1091 | FrRnd | 25 | Indians | Ryan Miller (minors) | | | | | | | | | | | | | JC | Blinn College (Brenham, TX) |
| 2006 | 37 | | 1108 | FrRnd | 12 | Rangers | John Lambert (minors) | | | | | | | | | | | | | HS | Chesterton HS (Chesterton, IN) |
| 2006 | 37 | | 1123 | FrRnd | 27 | Red Sox | Justin Marks (minors) | | | | | | | | | | | | | HS | Catholic HS (Owensboro, KY) |
| 2006 | 38 | | 1128 | FrRnd | 2 | Rockies | Jon Hesketh (minors) | | | | | | | | | | | | | JC | Vernon College (Vernon, TX) |
| 2006 | 38 | | 1142 | FrRnd | 16 | Brewers | Todd Fitzgerald (minors) | | | | | | | | | | | | | JC | San Jose City College (San Jose, CA) |
| 2006 | 39 | | 1158 | FrRnd | 2 | Rockies | Jason Fuqua (minors) | | | | | | | | | | | | | HS | Sterling HS (Houston, TX) |
| 2006 | 39 | | 1163 | FrRnd | 7 | Dodgers | Jake Debus (minors) | | | | | | | | | | | | | JC | Moraine Valley Community College (Palos Hills, IL) |
| 2006 | 39 | | 1165 | FrRnd | 9 | Orioles | Neal Davis (minors) | | | | | | | | | | | | | HS | Catonsville HS (Catonsville, MD) |
| 2006 | 39 | | 1173 | FrRnd | 17 | Padres | Chance Deason (minors) | | | | | | | | | | | | | HS | Piedmont HS (Piedmont, OK) |
| 2006 | 39 | | 1181 | FrRnd | 25 | Indians | James Brettl (minors) | | | | | | | | | | | | | 4Yr | California State University Northridge (Los Angeles, CA) |
| 2006 | 39 | | 1186 | FrRnd | 30 | Cardinals | Matt Michael (minors) | | | | | | | | | | | | | 4Yr | Grand Canyon University (Phoenix, AZ) |
| 2006 | 40 | | 1187 | FrRnd | 1 | Royals | Christopher Snipes (minors) | | | | | | | | | | | | | HS | Warner Robins HS (Warner Robins, GA) |
| 2006 | 40 | | 1203 | FrRnd | 17 | Padres | Joshua Casas (minors) | | | | | | | | | | | | | HS | South El Monte HS (South El Monte, CA) |
| 2006 | 40 | | 1207 | FrRnd | 21 | Phillies | Nathan Solow (minors) | | | | | | | | | | | | | HS | La Cueva HS (Albuquerque, NM) |
| 2006 | 40 | | 1214 | FrRnd | 28 | Yankees | Tanner Chitwood (minors) | | | | | | | | | | | | | HS | Sulphur HS (Sulphur, OK) |
| 2006 | 41 | | 1227 | FrRnd | 11 | Diamondbacks | Quinton Marsh (minors) | | | | | | | | | | | | | HS | Wickenburg HS (Wickenburg, AZ) |
| 2006 | 41 | | 1237 | FrRnd | 21 | Phillies | Mike Antonini (minors) | | | | | | | | | | | | | 4Yr | Georgia College and State University (Milledgeville, GA) |
| 2006 | 42 | | 1250 | FrRnd | 4 | Pirates | Jonathan Harmston (minors) | | | | | | | | | | | | | HS | Bullard HS (Fresno, CA) |
| 2006 | 42 | | 1252 | FrRnd | 6 | Tigers | Kevin Chapman (minors) | | | | | | | | | | | | | HS | Westminster Academy (Fort Lauderdale, FL) |
| 2006 | 42 | | 1255 | FrRnd | 9 | Orioles | Jordan Durrance (minors) | | | | | | | | | | | | | HS | Sierra HS (Tollhouse, CA) |
| 2006 | 42 | | 1269 | FrRnd | 23 | Braves | Ralph West (minors) | | | | | | | | | | | | | HS | Garfield HS (Woodbridge, VA) |
| 2006 | 42 | | 1272 | FrRnd | 26 | Red Sox | Troy Graybill (minors) | | | | | | | | | | | | | HS | Sarasota HS (Sarasota, FL) |
| 2006 | 43 | | 1300 | FrRnd | 25 | Angels | Doug Brandt (minors) | | | | | | | | | | | | | 4Yr | California State University San Bernardino (San Bernardino, CA) |
| 2006 | 43 | | 1302 | FrRnd | 27 | Yankees | Eric Erickson (minors) | | | | | | | | | | | | | HS | Sarasota HS (Sarasota, FL) |
| 2006 | 44 | | 1306 | FrRnd | 2 | Rockies | Scott Bachman (minors) | | | | | | | | | | | | | HS | Rocky Mountain HS (Fort Collins, CO) |
| 2006 | 44 | | 1319 | FrRnd | 15 | Nationals | Chad Jenkins (minors) | | | | | | | | | | | | | HS | Caravel Academy (Bear, DE) |
| 2006 | 45 | | 1340 | FrRnd | 7 | Dodgers | Greg Hendrix (minors) | | | | | | | | | | | | | HS | North Atlanta HS (Atlanta, GA) |
| 2006 | 45 | | 1341 | FrRnd | 8 | Reds | Michael Lachapelle (minors) | | | | | | | | | | | | | HS | Sahuaro HS (Tucson, AZ) |
| 2006 | 45 | | 1345 | FrRnd | 12 | Rangers | Danny Herrera (minors) | 0.3 | 131 | 3 | 0 | .000 | .250 | 131 | 5 | 8 | 3.72 | 1.50 | 0 | 4Yr | University of New Mexico (Albuquerque, NM) |
| 2006 | 45 | | 1347 | FrRnd | 14 | Blue Jays | Lee Verweel (minors) | | | | | | | | | | | | | HS | Malvern Collegiate Institute (Toronto, ON) |
| 2006 | 45 | | 1358 | FrRnd | 25 | Angels | Matthew McCracken (minors) | | | | | | | | | | | | | JC | Florida College (Jacksonville, FL) |
| 2006 | 46 | | 1372 | FrRnd | 10 | Giants | Taylor Hammack (minors) | | | | | | | | | | | | | HS | Angleton HS (Angleton, TX) |
| 2006 | 46 | | 1375 | FrRnd | 13 | Cubs | Ryan Shook (minors) | | | | | | | | | | | | | HS | Valley Christian Academy (Santa Maria, CA) |
| 2006 | 46 | | 1376 | FrRnd | 14 | Blue Jays | Mace Thurman (minors) | | | | | | | | | | | | | JC | McLennan Community College (Waco, TX) |
| 2006 | 47 | | 1399 | FrRnd | 9 | Orioles | Troy Burki (minors) | | | | | | | | | | | | | HS | Gig Harbor HS (Gig Harbor, WA) |
| 2006 | 47 | | 1400 | FrRnd | 10 | Giants | Ryan Bradley (minors) | | | | | | | | | | | | | HS | Mattoon HS (Mattoon, IL) |
| 2006 | 47 | | 1415 | FrRnd | 25 | Red Sox | Nick Hill (minors) | | | | | | | | | | | | | 4Yr | United States Military Academy (West Point, NY) |
| 2006 | 47 | | 1418 | FrRnd | 28 | Cardinals | Nick Additon (minors) | | | | | | | | | | | | | HS | Western HS (Davie, FL) |
| 2006 | 48 | | 1421 | FrRnd | 3 | Devil Rays | Alex McRee (minors) | | | | | | | | | | | | | HS | Chestatee HS (Chestatee, GA) |
| 2006 | 48 | | 1423 | FrRnd | 5 | Mariners | Jeremy Beeching (minors) | | | | | | | | | | | | | JC | Volunteer State Community College (Gallatin, TN) |
| 2006 | 48 | | 1439 | FrRnd | 21 | Astros | Jerry Quinones (minors) | | | | | | | | | | | | | JC | Compton Community College (Compton, CA) |
| 2006 | 48 | | 1446 | FrRnd | 28 | Cardinals | Garry Thomas (minors) | | | | | | | | | | | | | HS | Pine Bluff HS (Pine Bluff, AR) |
| 2006 | 49 | | 1461 | FrRnd | 15 | Nationals | Jarred Holloway (minors) | | | | | | | | | | | | | HS | Russellville HS (Russellville, AR) |
| 2006 | 49 | | 1466 | FrRnd | 20 | Phillies | Olivier Routhier-Pare (minors) | | | | | | | | | | | | | JC | Ahuntsic College (Cap-Rouge, QC) |
| 2006 | 50 | | 1486 | FrRnd | 12 | Rangers | Patrick Donovan (minors) | | | | | | | | | | | | | 4Yr | Gonzaga University (Spokane, WA) |
| 2006 | 50 | | 1487 | FrRnd | 13 | Cubs | Ryan Davis (minors) | | | | | | | | | | | | | HS | Eastlake HS (Sammamish, WA) |
| 2006 | 50 | | 1491 | FrRnd | 17 | Mets | Ryan Wolfe (minors) | | | | | | | | | | | | | HS | Winter Park HS (Winter Park, FL) |
| 2006 | 50 | | 1496 | FrRnd | 22 | Braves | Thomas Jordan (minors) | | | | | | | | | | | | | JC | Hinds Community College (Raymond, MS) |
| 2006 | 50 | | 1498 | FrRnd | 24 | Angels | Timothy Brewer (minors) | | | | | | | | | | | | | HS | Ivanna Eudora Kean HS (St. Thomas, VI) |