| 2005 | 1 | | 1 | FrRnd | 1 | Diamondbacks | Justin Upton (minors) | 16.3 | 777 | 2826 | 122 | .277 | .840 | | | | | | | HS | Great Bridge HS (Chesapeake, VA) |
| 2005 | 1 | | 7 | FrRnd | 7 | Rockies | Troy Tulowitzki (minors) | 29.4 | 787 | 2959 | 139 | .294 | .874 | | | | | | | 4Yr | California State University Long Beach (Long Beach, CA) |
| 2005 | 1 | | 17 | FrRnd | 17 | Yankees via Phillies | *C.J. Henry (minors) | | | | | | | | | | | | | HS | Putnam City HS (Oklahoma City, OK) |
| 2005 | 1 | | 21 | FrRnd | 21 | Athletics | Cliff Pennington (minors) | 7.0 | 563 | 1858 | 25 | .246 | .663 | | | | | | | 4Yr | Texas A&M University (College Station, TX) |
| 2005 | 1 | | 30 | FrRnd | 30 | Cardinals | Tyler Greene (minors) | -0.6 | 286 | 672 | 17 | .225 | .647 | | | | | | | 4Yr | Georgia Institute of Technology (Atlanta, GA) |
| 2005 | 2 | | 50 | FrRnd | 2 | Royals | Jeff Bianchi (minors) | -0.2 | 45 | 94 | 3 | .213 | .583 | | | | | | | HS | Lampeter-Strasburg HS (Lampeter, PA) |
| 2005 | 2 | | 51 | FrRnd | 3 | Dodgers via Mariners | *Ivan De Jesus (minors) | -0.8 | 48 | 73 | 0 | .205 | .500 | | | | | | | | |
| 2005 | 2 | | 54 | FrRnd | 6 | Twins via Blue Jays | *Paul Kelly (minors) | | | | | | | | | | | | | HS | Flower Mound HS (Flower Mound, TX) |
| 2005 | 2 | | 58 | FrRnd | 10 | Angels via Tigers | *Ryan Mount (minors) | | | | | | | | | | | | | HS | Senator Ruben S. Ayala HS (Chino Hills, CA) |
| 2005 | 2 | | 71 | FrRnd | 23 | Angels | P.J. Phillips (minors) | | | | | | | | | | | | | HS | Redan HS (Stone Mountain, GA) |
| 2005 | 2 | | 75 | FrRnd | 27 | Braves | Yunel Escobar (minors) | 20.0 | 826 | 3074 | 57 | .279 | .738 | | | | | | | | |
| 2005 | 2s | | 80 | FrRnd | 32 | Twins | *Drew Thompson (minors) | | | | | | | | | | | | | HS | Jupiter HS (Jupiter, FL) |
| 2005 | 3 | | 89 | FrRnd | 9 | Astros via Mets | *Tommy Manzella (minors) | -1.3 | 90 | 263 | 1 | .224 | .528 | | | | | | | 4Yr | Tulane University (New Orleans, LA) |
| 2005 | 4 | | 121 | FrRnd | 11 | Pirates | Brent Lillibridge (minors) | -0.5 | 347 | 673 | 19 | .207 | .609 | | | | | | | 4Yr | University of Washington (Seattle, WA) |
| 2005 | 4 | | 130 | FrRnd | 20 | Cubs | Dylan Johnston (minors) | | | | | | | | | | | | | HS | Hamilton HS (Chandler, AZ) |
| 2005 | 5 | | 142 | FrRnd | 2 | Royals | Shawn Hayes (minors) | | | | | | | | | | | | | 4Yr | Franklin Pierce University (Rindge, NH) |
| 2005 | 5 | | 158 | FrRnd | 18 | Padres | Seth Johnston (minors) | | | | | | | | | | | | | 4Yr | University of Texas at Austin (Austin, TX) |
| 2005 | 5 | | 165 | FrRnd | 25 | Twins | Steven Tolleson (minors) | -0.1 | 54 | 120 | 3 | .225 | .623 | | | | | | | 4Yr | University of South Carolina (Columbia, SC) |
| 2005 | 6 | | 190 | FrRnd | 20 | Cubs | Kyle Reynolds (minors) | | | | | | | | | | | | | 4Yr | Baylor University (Waco, TX) |
| 2005 | 6 | | 191 | FrRnd | 21 | Athletics | Justin Sellers (minors) | 0.8 | 81 | 235 | 3 | .200 | .581 | | | | | | | HS | Marina HS (Huntington Beach, CA) |
| 2005 | 7 | | 207 | FrRnd | 7 | Rockies | Geoff Strickland (minors) | | | | | | | | | | | | | 4Yr | Florida Southern College (Lakeland, FL) |
| 2005 | 7 | | 224 | FrRnd | 24 | Astros | Timothy Johnson (minors) | | | | | | | | | | | | | HS | Wissahickon Senior HS (Ambler, PA) |
| 2005 | 8 | | 235 | FrRnd | 5 | Brewers | Jemile Weeks (minors) | 0.8 | 215 | 850 | 4 | .260 | .681 | | | | | | | HS | Lake Brantley HS (Altamonte Springs, FL) |
| 2005 | 8 | | 242 | FrRnd | 12 | Reds | Michael Jones (minors) | | | | | | | | | | | | | HS | Wayne County HS (Jesup, GA) |
| 2005 | 8 | | 253 | FrRnd | 23 | Angels | Matthew Hall (minors) | | | | | | | | | | | | | HS | Horizon HS (Scottsdale, AZ) |
| 2005 | 9 | | 282 | FrRnd | 22 | Giants | Anthony Contreras (minors) | | | | | | | | | | | | | 4Yr | San Jose State University (San Jose, CA) |
| 2005 | 10 | | 297 | FrRnd | 7 | Rockies | Garner Wetzel (minors) | | | | | | | | | | | | | 4Yr | Millsaps College (Jackson, MS) |
| 2005 | 10 | | 310 | FrRnd | 20 | Cubs | Joe Simokaitis (minors) | | | | | | | | | | | | | 4Yr | University of Nebraska at Lincoln (Lincoln, NE) |
| 2005 | 11 | | 326 | FrRnd | 6 | Blue Jays | Wesley Stone (minors) | | | | | | | | | | | | | HS | A. B. Miller HS (Fontana, CA) |
| 2005 | 12 | | 362 | FrRnd | 12 | Reds | Adam Rosales (minors) | 1.7 | 274 | 741 | 17 | .228 | .641 | | | | | | | 4Yr | Western Michigan University (Kalamazoo, MI) |
| 2005 | 12 | | 364 | FrRnd | 14 | Indians | Matt Fornasiere (minors) | | | | | | | | | | | | | 4Yr | University of Minnesota (Minneapolis, MN) |
| 2005 | 13 | | 383 | FrRnd | 3 | Mariners | Reed Eastley (minors) | | | | | | | | | | | | | 4Yr | Niagara University (Lewiston, NY) |
| 2005 | 13 | | 390 | FrRnd | 10 | Tigers | Louis Ott (minors) | | | | | | | | | | | | | JC | Sacramento City College (Sacramento, CA) |
| 2005 | 13 | | 404 | FrRnd | 24 | Astros | Eric King (minors) | | | | | | | | | | | | | 4Yr | University of Tennessee (Knoxville, TN) |
| 2005 | 14 | | 428 | FrRnd | 18 | Padres | Billy Richardson (minors) | | | | | | | | | | | | | 4Yr | East Carolina University (Greenville, NC) |
| 2005 | 14 | | 438 | FrRnd | 28 | Red Sox | Pedro Alvarez (minors) | 1.1 | 360 | 1250 | 58 | .231 | .724 | | | | | | | HS | Horace Mann School (Riverdale, NY) |
| 2005 | 15 | | 456 | FrRnd | 16 | Marlins | Paul Witt (minors) | | | | | | | | | | | | | 4Yr | Baylor University (Waco, TX) |
| 2005 | 15 | | 457 | FrRnd | 17 | Phillies | P.J. Antoniato (minors) | | | | | | | | | | | | | 4Yr | St. John's University (Queens, NY) |
| 2005 | 16 | | 478 | FrRnd | 8 | Devil Rays | Neil Walton (minors) | | | | | | | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 2005 | 16 | | 480 | FrRnd | 10 | Tigers | Michael Hollimon (minors) | 0.2 | 11 | 23 | 1 | .261 | .845 | | | | | | | 4Yr | Oral Roberts University (Tulsa, OK) |
| 2005 | 17 | | 502 | FrRnd | 2 | Royals | Miguel Vasquez (minors) | | | | | | | | | | | | | HS | DeWitt Clinton HS (Bronx, NY) |
| 2005 | 17 | | 528 | FrRnd | 28 | Red Sox | Dominic Ramos (minors) | | | | | | | | | | | | | 4Yr | Texas State University (San Marcos, TX) |
| 2005 | 18 | | 542 | FrRnd | 12 | Reds | Kevyn Feiner (minors) | | | | | | | | | | | | | HS | Sun Prairie HS (Sun Prairie, WI) |
| 2005 | 18 | | 546 | FrRnd | 16 | Marlins | Kyle Padgett (minors) | | | | | | | | | | | | | 4Yr | College of William and Mary (Williamsburg, VA) |
| 2005 | 18 | | 549 | FrRnd | 19 | Rangers | Chase Fontaine (minors) | | | | | | | | | | | | | JC | Daytona Beach Community College (Daytona Beach, FL) |
| 2005 | 18 | | 556 | FrRnd | 26 | Dodgers | Kevin Carby (minors) | | | | | | | | | | | | | HS | Booker T. Washington HS (Tulsa, OK) |
| 2005 | 18 | | 560 | FrRnd | 30 | Cardinals | Brandon Garner (minors) | | | | | | | | | | | | | HS | Yale HS (Yale, MI) |
| 2005 | 19 | | 572 | FrRnd | 12 | Reds | Eric Eymann (minors) | | | | | | | | | | | | | 4Yr | Kansas State University (Manhattan, KS) |
| 2005 | 19 | | 587 | FrRnd | 27 | Braves | Cole Miles (minors) | | | | | | | | | | | | | HS | Viewmont HS (Bountiful, UT) |
| 2005 | 20 | | 603 | FrRnd | 13 | Orioles | Ryan Steinbach (minors) | | | | | | | | | | | | | 4Yr | Indiana University/Purdue University at Fort Wayne (Fort Wayne, IN) |
| 2005 | 20 | | 615 | FrRnd | 25 | Twins | Eric Santiago (minors) | | | | | | | | | | | | | | |
| 2005 | 21 | | 630 | FrRnd | 10 | Tigers | David Adams (minors) | | | | | | | | | | | | | HS | Grandview Prep (Boca Raton, FL) |
| 2005 | 21 | | 631 | FrRnd | 11 | Pirates | Elias Otero (minors) | | | | | | | | | | | | | | |
| 2005 | 21 | | 646 | FrRnd | 26 | Dodgers | Shane Justis (minors) | | | | | | | | | | | | | 4Yr | Towson University (Towson, MD) |
| 2005 | 21 | | 650 | FrRnd | 30 | Cardinals | Ryan Rohlinger (minors) | -0.9 | 46 | 67 | 0 | .134 | .377 | | | | | | | 4Yr | University of Oklahoma (Norman, OK) |
| 2005 | 22 | | 652 | FrRnd | 2 | Royals | Justin Bristow (minors) | | | | | | | | | | | | | HS | Mills E Godwin HS (Richmond, VA) |
| 2005 | 22 | | 657 | FrRnd | 7 | Rockies | Radames Nazario (minors) | | | | | | | | | | | | | | |
| 2005 | 23 | | 690 | FrRnd | 10 | Tigers | Mark Haske (minors) | | | | | | | | | | | | | 4Yr | University of Cincinnati (Cincinnati, OH) |
| 2005 | 23 | | 697 | FrRnd | 17 | Phillies | Derrick Mitchell (minors) | | | | | | | | | | | | | HS | Paw Paw HS (Paw Paw, MI) |
| 2005 | 24 | | 712 | FrRnd | 2 | Royals | Josh Colafemina (minors) | | | | | | | | | | | | | 4Yr | College of St. Rose (Albany, NY) |
| 2005 | 24 | | 723 | FrRnd | 13 | Orioles | Stuart Musslewhite (minors) | | | | | | | | | | | | | 4Yr | Texas Christian University (Fort Worth, TX) |
| 2005 | 24 | | 730 | FrRnd | 20 | Cubs | Scott Hode (minors) | | | | | | | | | | | | | 4Yr | University of Arkansas (Fayetteville, AR) |
| 2005 | 24 | | 731 | FrRnd | 21 | Athletics | Ben Ingold (minors) | | | | | | | | | | | | | 4Yr | Wake Forest University (Winston-Salem, NC) |
| 2005 | 25 | | 744 | FrRnd | 4 | Nationals | Josue Peley (minors) | | | | | | | | | | | | | | |
| 2005 | 25 | | 746 | FrRnd | 6 | Blue Jays | Philip Carey (minors) | | | | | | | | | | | | | | |
| 2005 | 25 | | 754 | FrRnd | 14 | Indians | Andrew Lytle (minors) | | | | | | | | | | | | | 4Yr | University of Iowa (Iowa City, IA) |
| 2005 | 25 | | 761 | FrRnd | 21 | Athletics | Zeke Parraz (minors) | | | | | | | | | | | | | 4Yr | University of Nevada-Las Vegas (Las Vegas, NV) |
| 2005 | 26 | | 771 | FrRnd | 1 | Diamondbacks | Brian Chavez (minors) | | | | | | | | | | | | | JC | College of the Canyons (Santa Clarita, CA) |
| 2005 | 26 | | 776 | FrRnd | 6 | Blue Jays | Marshall Bernhard (minors) | | | | | | | | | | | | | 4Yr | University of Central Florida (Orlando, FL) |
| 2005 | 26 | | 796 | FrRnd | 26 | Dodgers | Jordy Mercer (minors) | 1.0 | 57 | 108 | 4 | .231 | .705 | | | | | | | HS | Taloga HS (Taloga, OK) |
| 2005 | 28 | | 835 | FrRnd | 5 | Brewers | Scott McKnight (minors) | | | | | | | | | | | | | JC | Saddleback College (Mission Viejo, CA) |
| 2005 | 29 | | 867 | FrRnd | 7 | Rockies | Reese Havens (minors) | | | | | | | | | | | | | HS | Bishop England HS (Charleston, SC) |
| 2005 | 29 | | 882 | FrRnd | 22 | Giants | Angel Nicolas (minors) | | | | | | | | | | | | | HS | Killian HS (Miami, FL) |
| 2005 | 30 | | 897 | FrRnd | 7 | Rockies | Michael Milliron (minors) | | | | | | | | | | | | | 4Yr | Pennsylvania State University (State College, PA) |
| 2005 | 31 | | 922 | FrRnd | 2 | Royals | Pedro Lopez (minors) | | | | | | | | | | | | | 4Yr | Turabo University (Gurabo, PR) |
| 2005 | 31 | | 928 | FrRnd | 8 | Devil Rays | Jordan Brown (minors) | | | | | | | | | | | | | HS | Hahnville HS (Hahnville, LA) |
| 2005 | 31 | | 950 | FrRnd | 30 | Cardinals | Christian Lopez (minors) | | | | | | | | | | | | | | |
| 2005 | 32 | | 958 | FrRnd | 8 | Devil Rays | Ryan Bethel (minors) | | | | | | | | | | | | | 4Yr | Grand Canyon University (Phoenix, AZ) |
| 2005 | 32 | | 959 | FrRnd | 9 | Mets | Jose Castro (minors) | | | | | | | | | | | | | JC | Miami-Dade College (Miami, FL) |
| 2005 | 32 | | 969 | FrRnd | 19 | Rangers | Renny Osuna (minors) | | | | | | | | | | | | | JC | New Mexico Junior College (Hobbs, NM) |
| 2005 | 33 | | 995 | FrRnd | 15 | White Sox | Scott Savastano (minors) | | | | | | | | | | | | | HS | Plymouth North HS (Plymouth, MA) |
| 2005 | 33 | | 1003 | FrRnd | 23 | Angels | Marco Albano (minors) | | | | | | | | | | | | | 4Yr | Boston College (Chestnut Hill, MA) |
| 2005 | 34 | | 1018 | FrRnd | 8 | Devil Rays | Matthew Devins (minors) | | | | | | | | | | | | | 4Yr | Stony Brook University (Stony Brook, NY) |
| 2005 | 34 | | 1035 | FrRnd | 25 | Twins | Daniel Cox (minors) | | | | | | | | | | | | | HS | W. F. West HS (Chehalis, WA) |
| 2005 | 35 | | 1061 | FrRnd | 21 | Athletics | Steve Braun (minors) | | | | | | | | | | | | | JC | Los Angeles Pierce College (Woodland Hills, CA) |
| 2005 | 36 | | 1091 | FrRnd | 21 | Athletics | Shane Keough (minors) | | | | | | | | | | | | | HS | Northwood HS (Irvine, CA) |
| 2005 | 38 | | 1144 | FrRnd | 14 | Indians | Daniel Lima (minors) | | | | | | | | | | | | | HS | Florida Christian School (Miami, FL) |
| 2005 | 39 | | 1165 | FrRnd | 5 | Brewers | Brad Miller (minors) | | | | | | | | | | | | | JC | Cowley County Community College (Arkansas City, KS) |
| 2005 | 39 | | 1175 | FrRnd | 15 | White Sox | Jovan Rosa (minors) | | | | | | | | | | | | | HS | East Hartford HS (East Hartford, CT) |
| 2005 | 40 | | 1191 | FrRnd | 2 | Royals | Nicholas Romero (minors) | | | | | | | | | | | | | HS | Eastlake HS (Chula Vista, CA) |
| 2005 | 40 | | 1194 | FrRnd | 5 | Brewers | Ryan Crew (minors) | | | | | | | | | | | | | 4Yr | University of Texas at San Antonio (San Antonio, TX) |
| 2005 | 40 | | 1201 | FrRnd | 12 | Reds | Angel Cabrera (minors) | | | | | | | | | | | | | JC | Connors State College (Warner, OK) |
| 2005 | 41 | | 1220 | FrRnd | 2 | Royals | Anthony Rodriguez (minors) | | | | | | | | | | | | | | |
| 2005 | 41 | | 1230 | FrRnd | 12 | Reds | Justin Tordi (minors) | | | | | | | | | | | | | 4Yr | University of Florida (Gainesville, FL) |
| 2005 | 41 | | 1235 | FrRnd | 17 | Phillies | Ryan Selden (minors) | | | | | | | | | | | | | HS | Canyon Springs HS (Moreno Valley, CA) |
| 2005 | 41 | | 1239 | FrRnd | 21 | Giants | Bo Merrell (minors) | | | | | | | | | | | | | HS | Perryton HS (Perryton, TX) |
| 2005 | 41 | | 1242 | FrRnd | 24 | Twins | Toby Gardenhire (minors) | | | | | | | | | | | | | 4Yr | University of Illinois at Urbana-Champaign (Champaign, IL) |
| 2005 | 41 | | 1247 | FrRnd | 29 | Cardinals | David Fonseca (minors) | | | | | | | | | | | | | HS | Thousand Oaks HS (Thousand Oaks, CA) |
| 2005 | 42 | | 1254 | FrRnd | 7 | Rockies | Maikol Gonzalez (minors) | | | | | | | | | | | | | JC | Louisburg College (Louisburg, NC) |
| 2005 | 42 | | 1265 | FrRnd | 18 | Padres | Terrence Dayleg (minors) | | | | | | | | | | | | | | |
| 2005 | 43 | | 1285 | FrRnd | 9 | Mets | Javier Brown (minors) | | | | | | | | | | | | | HS | Valhalla HS (El Cajon, CA) |
| 2005 | 43 | | 1286 | FrRnd | 10 | Tigers | Ryan Perry (minors) | | | | | | | | | | | | | HS | Rocklin HS (Rocklin, CA) |
| 2005 | 44 | | 1320 | FrRnd | 15 | White Sox | Drew George (minors) | | | | | | | | | | | | | JC | Lower Columbia College (Longview, WA) |
| 2005 | 44 | | 1330 | FrRnd | 25 | Dodgers | Chase d'Arnaud (minors) | -0.6 | 56 | 149 | 0 | .208 | .507 | | | | | | | HS | Los Alamitos HS (Los Alamitos, CA) |
| 2005 | 45 | | 1358 | FrRnd | 24 | Twins | Michael Kinsel (minors) | | | | | | | | | | | | | HS | Cretin HS (St. Paul, MN) |
| 2005 | 46 | | 1372 | FrRnd | 9 | Mets | Pete Tountas (minors) | | | | | | | | | | | | | HS | Maine South HS (Park Ridge, IL) |
| 2005 | 46 | | 1377 | FrRnd | 14 | Indians | Blake Davis (minors) | 0.1 | 25 | 59 | 1 | .254 | .713 | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 2005 | 46 | | 1389 | FrRnd | 26 | Braves | Luis Sanchez (minors) | | | | | | | | | | | | | JC | Florida Gateway College (Lake City, FL) |
| 2005 | 47 | | 1403 | FrRnd | 11 | Pirates | Ryan Lormand (minors) | | | | | | | | | | | | | JC | McLennan Community College (Waco, TX) |
| 2005 | 47 | | 1409 | FrRnd | 17 | Phillies | Ben Blanton (minors) | | | | | | | | | | | | | JC | William Jewell College (Liberty, MO) |
| 2005 | 49 | | 1461 | FrRnd | 14 | Indians | Ryan Wood (minors) | | | | | | | | | | | | | HS | Hylton HS (Hylton, VA) |
| 2005 | 50 | | 1475 | FrRnd | 1 | Diamondbacks | Ritchie Franklin (minors) | | | | | | | | | | | | | HS | Thompson HS (Alabaster, AL) |
| 2005 | 50 | | 1492 | FrRnd | 18 | Padres | Jason Ogata (minors) | | | | | | | | | | | | | HS | Westview HS (Portland, OR) |