| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 1 | 1 | 1 | Tidewater | Ryan Zimmerman | 3B |
| 2 | 1 | 2 | East Coast | Francisco Liriano | P |
| 3 | 1 | 3 | Beantown | Chien-Ming Wang | P |
| 4 | 1 | 4 | Shenandoah | Kirk Saaroos | P |
| 5 | 1 | 5 | San Diego | Kenji Johjima | C |
| 6 | 1 | 6 | Arundel (from Rhode Island) |
Ervin Santana | P |
| 7 | 1 | 7 | Buffalo | Emil Brown | OF |
| 8 | 1 | 8 | Stamford | Aaron Hill | 3B |
| 9 | 1 | 9 | Jonesboro | Aaron Fultz | P |
| 10 | 1 | 10 | Tampa | Cory Sullivan | P |
| 11 | 1 | 11 | Brooklyn Ave | Paul Malholm | P |
| 12 | 1 | 12 | Arundel | Brian McCann | C |
| 13 | 1 | 13 | Green Bay | Bobby Jenks | P |
| 14 | 1 | 14 | Texas | Edison Volquez | P |
| 15 | 1 | 15 | Greensboro | Freddy Sanchez | 3B |
| 16 | 1 | 16 | Westchester | Jason Vargas | P |
| 17 | 1 | 17 | Shenandoah (from Cleveland) |
Ronny Cedeno | SS |
| 18 | 1 | 18 | Freeport | Hector Carrasco | P |
| 19 | 1 | 19 | Turtle Beach | Brian Fuentes | P |
| 20 | 1 | 20 | Baton Rouge | Aaron Small | P |
| 21 | 1 | 21 | Glab | Justin Upton (prospect) |
SS |
| 22 | 1 | 22 | Chappaqua | Robinson Tejeda | P |
| 23 | 1 | 23 | Mokena | Mike MacDougal | P |
| 24 | 1 | 24 | Louisiana | Brandon Wood (prospect) |
SS |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 25 | 2 | 1 | Tidewater | Chris Young (prospect) |
OF |
| 26 | 2 | 2 | East Coast | Ryan Doumit | C |
| 27 | 2 | 3 | Beantown | Clay Hensley | P |
| 28 | 2 | 4 | Shenandoah | Chris Duffy | OF |
| 29 | 2 | 5 | San Diego | Mike Jacobs | 1B |
| 30 | 2 | 6 | East Coast (from Rhode Island) |
Howie Kendrick (prospect) |
2B |
| 31 | 2 | 7 | Buffalo | Bob Wickman | P |
| 32 | 2 | 8 | Stamford | Matt Murton | OF |
| 33 | 2 | 9 | Jonesboro | Chuck James | P |
| 34 | 2 | 10 | Tampa | Mark Redman | P |
| 35 | 2 | 11 | Brooklyn Ave | Billy Butler (prospect) |
OF |
| 36 | 2 | 12 | Arundel | Jon Lester (prospect) |
P |
| 37 | 2 | 13 | Green Bay | Andy Phillips | 1B |
| 38 | 2 | 14 | Texas | Thomas Diamond (prospect) |
P |
| 39 | 2 | 15 | Greensboro | Brad Hennessey | P |
| 40 | 2 | 16 | Freeport (from Westchester) |
Kelly Johnson | OF |
| 41 | 2 | 17 | Shenandoah (from Cleveland) |
Willy Aybar | 3B |
| 42 | 2 | 18 | Rhode Island (from Freeport) |
Chris Ray | P |
| 43 | 2 | 19 | Turtle Beach | Gary Majewski | P |
| 44 | 2 | 20 | Baton Rouge | Pedro Astacio | P |
| 45 | 2 | 21 | Glab | Roberto Hernandez | P |
| 46 | 2 | 22 | Chappaqua | Pete Orr |
2B |
| 47 | 2 | 23 | Mokena | Rocco Baldelli (uncarded) |
OF |
| 48 | 2 | 24 | Louisiana | Alex Gordon (prospect) |
3B |
| Overall Pick |
Round number |
Pick number |
Player Selected | Pos | |
| 49 | 3 | 1 | Tidewater | Jarrod Saltalmacchia (prospect) |
C |
| 50 | 3 | 2 | Mokena (from East Coast) |
Danny Ardoin | C |
| 51 | 3 | 3 | Beantown | Fernando Cabrera | P |
| 52 | 3 | 4 | Cleveland (from Shenandoah) |
Jeff Fassero | P |
| 53 | 3 | 5 | San Diego | Chris Spurling | P |
| 54 | 3 | 6 | Rhode Island | John Rodriguez | OF |
| 55 | 3 | 7 | Buffalo | John Wasdin | P |
| 56 | 3 | 8 | Turtle Beach (from Stamford) |
Juan Padilla | P |
| 57 | 3 | 9 | Jonesboro | Chad Moeller | C |
| 58 | 3 | 10 | Tampa | Miguel Batista | P |
| 59 | 3 | 11 | Brooklyn Ave | Rick Helling | P |
| 60 | 3 | 12 | Arundel | Chad Orvella | P |
| 61 | 3 | 13 | Green Bay | JP Howell | P |
| 62 | 3 | 14 | Texas | Matt Guerrier | P |
| 63 | 3 | 15 | Mokena (from Greensboro) |
Fernando Rodney | P |
| 64 | 3 | 16 | Westchester | Larry Bigbie | OF |
| 65 | 3 | 17 | Cleveland | Will Ohman | P |
| 66 | 3 | 18 | Freeport | Josh Johnson | P |
| 67 | 3 | 19 | Turtle Beach | Jack Taschner | P |
| 68 | 3 | 20 | Baton Rouge | Wandy Rodriguez | P |
| 69 | 3 | 21 | Glab | Pete Walker | P |
| 70 | 3 | 22 | Arundel (from Chappaqua) |
Cesar Carillo (prospect) |
P |
| 71 | 3 | 23 | East Coast (from Stamford through Mokena) |
Neil Walker (prospect) |
C |
| 72 | 3 | 24 | Louisiana | Brandon Medders | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 73 | 4 | 1 | Tidewater | Justin Huber | 1B |
| 74 | 4 | 2 | East Coast | Ian Kinsler (prospect) |
2B |
| 75 | 4 | 3 | Beantown | Scott Munter | P |
| 76 | 4 | 4 | Shenandoah | Rene Rivera | C |
| 77 | 4 | 5 | San Diego | Robert Fick | 1B |
| 78 | 4 | 6 | Rhode Island | Joe Mays | P |
| 79 | 4 | 7 | Buffalo | DJ Carrasco | P |
| 80 | 4 | 8 | Stamford | Brian Shackleford | P |
| 81 | 4 | 9 | Jonesboro | Chris Widger | C |
| 82 | 4 | 10 | Tampa | Sal Fasano | C |
| 83 | 4 | 11 | Brooklyn Ave | Geoff Geary | P |
| 84 | 4 | 12 | Arundel | Ambiorix Burgos | P |
| 85 | 4 | 13 | Green Bay | Ben Johnson | OF |
| 86 | 4 | 14 | East Coast (from Texas) |
Matt Miller | P |
| 87 | 4 | 15 | Westchester (from Greensboro) |
Russ Martin (prospect) |
C |
| 88 | 4 | 16 | Westchester | John Grabow | P |
| 89 | 4 | 17 | Cleveland | Randy Flores | P |
| 90 | 4 | 18 | Freeport | Felix Pie (prospect) |
OF |
| 91 | 4 | 19 | Turtle Beach | Ian Stewart (prospect) |
3B |
| 92 | 4 | 20 | Baton Rouge | Mike Morse | SS |
| 93 | 4 | 21 | Glab | Oscar Robles | SS |
| 94 | 4 | 22 | East Coast (from Chappaqua) |
Jamie Walker | P |
| 95 | 4 | 23 | Mokena | Joel Peralta | P |
| 96 | 4 | 24 | Louisiana | Hayden Penn | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 97 | 5 | 1 | Tidewater | Ryan Garko | C |
| 98 | 5 | 2 | East Coast | Jonathan Braxton | P |
| 99 | 5 | 3 | Beantown | Luis Rodriguez | 2B |
| 100 | 5 | 4 | Shenandoah | Marshall McDougall | 3B |
| 101 | 5 | 5 | San Diego | Chris Woodward | 1B |
| 102 | 5 | 6 | Rhode Island | Ezequiel Astacio | P |
| 103 | 5 | 7 | Buffalo | Damon Hollins | OF |
| 104 | 5 | 8 | Stamford | Dustin Nippert | P |
| 105 | 5 | 9 | Jonesboro | Doug Mientkiewicz | 1B |
| 106 | 5 | 10 | Tampa | Frank Thomas | 1B |
| 107 | 5 | 11 | Brooklyn Ave | Adam Miller (prospect) |
P |
| 108 | 5 | 12 | Arundel | Ryan Shealy | 1B |
| 109 | 5 | 13 | Green Bay | Ricky Nolasco (prospect) |
P |
| 110 | 5 | 14 | Texas | Tike Redman | OF |
| 111 | 5 | 15 | Greensboro | Claudio Vargas | P |
| 112 | 5 | 16 | Westchester | Keithe Foulke | P |
| 113 | 5 | 17 | Cleveland | Jeff Cirillo | 3B |
| 114 | 5 | 18 | Baton Rouge (from Freeport) |
Mike Edwards | 3B |
| 115 | 5 | 19 | Turtle Beach | Omar Infante | 2B |
| 116 | 5 | 20 | Baton Rouge | B. J. Surhoff | OF |
| 117 | 5 | 21 | Glab | Orlando Palmeiro | OF |
| 118 | 5 | 22 | East Coast (from Chappaqua) |
Craig Hansen | P |
| 119 | 5 | 23 | Mokena | Seth McClung | P |
| 120 | 5 | 24 | Louisiana | Anthony Lerew | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 121 | 6 | 1 | Tidewater | Anderson Hernandez | 2B |
| 122 | 6 | 2 | Stamford (from East Coast) |
Joe Borowski | P |
| 123 | 6 | 3 | Beantown | Nate McLouth | OF |
| 124 | 6 | 4 | Shenandoah | John-ford Griffin | OF |
| 125 | 6 | 5 | San Diego | John McDonald | SS |
| 126 | 6 | 6 | Tampa (from Freeport through Rhode Island) |
Corey Hart | OF |
| 127 | 6 | 7 | Buffalo | Gio Gonzalez (prospect) |
P |
| 128 | 6 | 8 | Stamford | Rich Hill | P |
| 129 | 6 | 9 | Jonesboro | Blaine Boyer | P |
| 130 | 6 | 10 | Tampa | Ramon Ortiz | P |
| 131 | 6 | 11 | Brooklyn Ave | Tom Gorzelanny | P |
| 132 | 6 | 12 | Arundel | Junior Spivey | 2B |
| 133 | 6 | 13 | Green Bay | Aaron Guiel | OF |
| 134 | 6 | 14 | Texas | Jason Repko | OF |
| 135 | 6 | 15 | Greensboro | Jason Hirsh (prospect) |
P |
| 136 | 6 | 16 | Westchester | Nick Markakis (prospect) |
OF |
| 137 | 6 | 17 | Cleveland | Ruben Gotay | 2B |
| 138 | 6 | 18 | Westchester (from Freeport) |
Russ Springer | P |
| 139 | 6 | 19 | Turtle Beach | Eduardo Perez | 1B |
| 140 | 6 | 20 | Baton Rouge | Rick White | P |
| 141 | 6 | 21 | Glab | Pablo Ozuna | 3B |
| 142 | 6 | 22 | Louisiana (from Arundel through Chappaqua) |
Omar Quintanilla | SS |
| 143 | 6 | 23 | Mokena | Dustan Mohr | OF |
| 144 | 6 | 24 | Louisiana | Jay Bergmann | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 145 | 7 | 1 | Tidewater | Franklin Gutierrez | OF |
| 146 | 7 | 2 | East Coast | Mike Gallo | P |
| 147 | 7 | 3 | Beantown | John Olerud | 1B |
| 148 | 7 | 4 | Shenandoah | Terry Tiffee | 3B |
| 149 | 7 | 5 | San Diego | Humberto Quintero | C |
| 150 | 7 | 6 | Rhode Island | Dan Uggla (prospect) |
2B |
| 151 | 7 | 7 | Buffalo | Greg Golson (prospect) |
OF |
| 152 | 7 | 8 | Stamford | Chris Denorfia | OF |
| 153 | 7 | 9 | Jonesboro | Sergio Mitre | P |
| 154 | 7 | 10 | Tampa | Jason Hammel (prospect) |
P |
| 155 | 7 | 11 | Brooklyn Ave | James Baldwin | P |
| 156 | 7 | 12 | Arundel | Joe Kennedy | P |
| 157 | 7 | 13 | Green Bay | Roberto Novoa | P |
| 158 | 7 | 14 | Texas | David Cortes | P |
| 159 | 7 | 15 | Rhode Island (from Greensboro) |
Jeremy Sowers (prospect) |
P |
| 160 | 7 | 16 | Westchester | Shane Victorino | OF |
| 161 | 7 | 17 | Cleveland | Terry Mulholland | P |
| 162 | 7 | 18 | Freeport | Rafael Soriano | P |
| 163 | 7 | 19 | Stamford (from Turtle Beach) |
George Kottaras (prospect) |
C |
| 164 | 7 | 20 | Baton Rouge | Paul Quantrill | P |
| 165 | 7 | 21 | Glab | Brad Eldred | 1B |
| 166 | 7 | 22 | Chappaqua | Craig Dingman | P |
| 167 | 7 | 23 | Mokena | Jose Macias | 3B |
| 168 | 7 | 24 | Louisiana | Eric Milton | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 169 | 8 | 1 | Tidewater | Joey Devine | P |
| 170 | 8 | 2 | East Coast | Jose Vizcaino | 2B |
| 171 | 8 | 3 | Beantown | Lenny Dinardo | P |
| 172 | 8 | 4 | Shenandoah | Robert Andino | SS |
| 173 | 8 | 5 | San Diego | Eli Whiteside | C |
| 174 | 8 | 6 | Rhode Island | Travis Bowyer | P |
| 175 | 8 | 7 | Buffalo | Geronimo Gil | C |
| 176 | 8 | 8 | East Coast (from Stamford) |
Brian Moehler | P |
| 177 | 8 | 9 | Jonesboro | Waiver Loss | |
| 178 | 8 | 10 | Tampa | Guillermo Quiroz | C |
| 179 | 8 | 11 | Brooklyn Ave | Dana Eveland | P |
| 180 | 8 | 12 | Arundel | Ricky Ledee | OF |
| 181 | 8 | 13 | Green Bay | Alberto Castillo | C |
| 182 | 8 | 14 | Texas | Lance Cormier | P |
| 183 | 8 | 15 | Greensboro | Todd Coffey | P |
| 184 | 8 | 16 | Westchester | Nelson Cruz | OF |
| 185 | 8 | 17 | Cleveland | Jeff Harris | P |
| 186 | 8 | 18 | Freeport | Adam Melhuse | C |
| 187 | 8 | 19 | Turtle Beach | Jeremy Accardo | P |
| 188 | 8 | 20 | Baton Rouge | Doug Brocail | P |
| 189 | 8 | 21 | Glab | Waiver Loss | |
| 190 | 8 | 22 | Chappaqua | Jody Gerut | OF |
| 191 | 8 | 23 | Mokena | John Parrish | P |
| 192 | 8 | 24 | Arundel (from Louisiana) |
Manny Delcarmen | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 193 | 9 | 1 | Tidewater | Marcos Carvajal | P |
| 194 | 9 | 2 | East Coast | George Sherill | P |
| 195 | 9 | 3 | Beantown | Andy LaRoche (prospect) |
IF |
| 196 | 9 | 4 | Shenandoah | Ricky Romero (prospect) |
P |
| 197 | 9 | 5 | San Diego | Andre Ethier (prospect) |
OF |
| 198 | 9 | 6 | Rhode Island | Phillip Hughes(prospect) | P |
| 199 | 9 | 7 | Buffalo | Mike Dejean | P |
| 200 | 9 | 8 | Stamford | Julio Santana | P |
| 201 | 9 | 9 | Tampa (from Jonesboro) |
Shinji Mori (prospect) |
P |
| 202 | 9 | 10 | Tampa | Miguel Ojeda | C |
| 203 | 9 | 11 | Brooklyn Ave | Troy Tulowitzki (prospect) |
SS |
| 204 | 9 | 12 | Arundel | Oscar Villarreal | P |
| 205 | 9 | 13 | Green Bay | Homer Bailey (prospect) |
P |
| 206 | 9 | 14 | Texas | Thomas Diamond (prospect) |
P |
| 207 | 9 | 15 | Greensboro | Matt Diaz | OF |
| 208 | 9 | 16 | Westchester | Erubiel Durazo | 1B |
| 209 | 9 | 17 | Cleveland | Pedro Lopez | 2B |
| 210 | 9 | 18 | Freeport | Jose Hernandez | 1B |
| 211 | 9 | 19 | Turtle Beach | Jeff Baker | 3B |
| 212 | 9 | 20 | Baton Rouge | John Halama | P |
| 213 | 9 | 21 | Beantown (from Glab) |
Jason Dubois | OF |
| 214 | 9 | 22 | Chappaqua | Scott Sauerbeck | P |
| 215 | 9 | 23 | Mokena | Fausto Carmona (prospect) |
P |
| 216 | 9 | 24 | Arundel (from Louisiana) |
Matt Capps | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 217 | 10 | 1 | Tidewater | Ryan Drese | P |
| 218 | 10 | 2 | Chappaqua (from East Coast) |
Vance Wilson | C |
| 219 | 10 | 3 | Beantown | Wade Townsend (prospect) |
P |
| 220 | 10 | 4 | Stamford (from Shenandoah) |
Matt Treanor | C |
| 221 | 10 | 5 | San Diego | Pass | |
| 222 | 10 | 6 | Rhode Island | Chip Ambres | OF |
| 223 | 10 | 7 | Buffalo | Lance Carter | P |
| 224 | 10 | 8 | Stamford | Anibal Sanchez (prospect) |
P |
| 225 | 10 | 9 | Texas (from Jonesboro) |
Jorge Julio | P |
| 226 | 10 | 10 | Tampa | Chris Snelling | OF |
| 227 | 10 | 11 | Brooklyn Ave | John Foster | P |
| 228 | 10 | 12 | Chappaqua (from Arundel) |
Dustin Pedroia (prospect) |
2B |
| 229 | 10 | 13 | Green Bay | Josh Kroeger (prospect) |
OF |
| 230 | 10 | 14 | Texas | Mike Stanton | P |
| 231 | 10 | 15 | Greensboro | Steve Schmoll |
P |
| 232 | 10 | 16 | Westchester | Chris Aguila | OF |
| 233 | 10 | 17 | Cleveland | Randy Ruiz (prospect) |
1B |
| 234 | 10 | 18 | Freeport | Matt Kemp (prospect) |
OF |
| 235 | 10 | 19 | Turtle Beach | Tony Giarratano | SS |
| 236 | 10 | 20 | Baton Rouge | Travis Harper | P |
| 237 | 10 | 21 | Glab | Waiver Loss | |
| 238 | 10 | 22 | Chappaqua | Andres Blanco | 2B |
| 239 | 10 | 23 | Mokena | Chad Bradford | P |
| 240 | 10 | 24 | Arundel (from Louisiana) |
Scott Williamson | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 241 | 11 | 1 | Tidewater | Franquelis Osoria | P |
| 242 | 11 | 2 | Chappaqua (from East Coast) |
Mike Pelfrey (prospect) |
P |
| 243 | 11 | 3 | Beantown | Eddy Garabito | 2B |
| 244 | 11 | 4 | Cleveland (from Shenandoah) |
David Maust (prospect) |
P |
| 245 | 11 | 5 | San Diego | Pass | |
| 246 | 11 | 6 | Rhode Island | Jaso Botts | OF |
| 247 | 11 | 7 | Buffalo | Chris Volstad (prospect) |
P |
| 248 | 11 | 8 | Stamford | Ryan Braun (prospect) |
3B |
| 249 | 11 | 9 | Texas (from Jonesboro) |
John Danks (prospect) |
P |
| 250 | 11 | 10 | Tampa | Eude Brito | P |
| 251 | 11 | 11 | Brooklyn Ave | Shane Costa | OF |
| 252 | 11 | 12 | Chappaqua (from Arundel) |
Tony Batista (uncarded) |
3B |
| 253 | 11 | 13 | Green Bay | Pass | |
| 254 | 11 | 14 | Texas | Jay Bruce (prospect) |
OF |
| 255 | 11 | 15 | Greensboro | Justin Lehr | P |
| 256 | 11 | 16 | Westchester | Erasmo Ramirez | P |
| 257 | 11 | 17 | Cleveland | Daniel Haigwood (prospect) |
P |
| 258 | 11 | 18 | Freeport | Pass | |
| 259 | 11 | 19 | Turtle Beach | Brent Clevlen (prospect) |
OF |
| 260 | 11 | 20 | Baton Rouge | Chan Ho Park | P |
| 261 | 11 | 21 | Glab | Waiver Loss | |
| 262 | 11 | 22 | Chappaqua | Paul Wilson | P |
| 263 | 11 | 23 | Mokena | Pass | |
| 264 | 11 | 24 | Louisiana | Melky Cabrera | OF |
|
|
|
|
|
|
| XTR | 1 | Jonesboro | James Jurries (prospect) |
1B | |
| XTR | 2 | Glab | Kaz Ishii | P | |
| XTR | 3 | Glab | Bobby Hill | 3B | |
| XTR | 4 | Glab | Michael Bourn (prospect) |
OF |