| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 1 | 1 | 1 | Long Island | Daisuke Matsuzaka (prospect) |
P |
| 2 | 1 | 2 | Greensboro | Ronnie Paulino | C |
| 3 | 1 | 3 | Tidewater | Chris Iannetta | C |
| 4 | 1 | 4 | Texas (from Westchester) | Adam Lind | OF |
| 5 | 1 | 5 | Texas | Matt Garza | P |
| 6 | 1 | 6 | Buffalo | Cla Meredith | P |
| 7 | 1 | 7 | Chappaqua | Takashi Saito | P |
| 8 | 1 | 8 | San Diego | Chris Duncan | OF |
| 9 | 1 | 9 | Jonesboro | Kevin Kouzmanoff | 3B |
| 10 | 1 | 10 | Stamford | Adam Wainwright | P |
| 11 | 1 | 11 | Baton Rouge | Luke Scott | OF |
| 12 | 1 | 12 | Millers Tavern (from Arundel) | Tim Lincecum (prospect) |
P |
| 13 | 1 | 13 | Rhode Island | Mark Derosa | 2B |
| 14 | 1 | 14 | Gulf Breeze | Marcus Thames | OF |
| 15 | 1 | 15 | Green Bay | Luke Hudson | P |
| 16 | 1 | 16 | Westchester (from Freeport) | Boof Bonser | P |
| 17 | 1 | 17 | Millers Tavern (from Tampa) | Andrew Miller | P |
| 18 | 1 | 18 | East Coast | James Shields | P |
| 19 | 1 | 19 | Turtle Beach | Yovani Gallardo (prospect) |
P |
| 20 | 1 | 20 | Beantown | Pedro Feliciano | P |
| 21 | 1 | 21 | Glab | Carlos Villanueva | P |
| 22 | 1 | 22 | Millers Tavern | Miguel Montero | C |
| 23 | 1 | 23 | Chappaqua (from Mokena) | Dennys Reyes | P |
| 24 | 1 | 24 | Louisiana | Jose Valentin | 2B |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 25 | 2 | 1 | Long Island | Mike Napoli | C |
| 26 | 2 | 2 | Greensboro | Sean Marshall | P |
| 27 | 2 | 3 | Tidewater | Reid Brignac (prospect) |
SS |
| 28 | 2 | 4 | Westchester | Scott Proctor | P |
| 29 | 2 | 5 | Texas | Adam Jones | OF |
| 30 | 2 | 6 | Buffalo | Chan Ho Park | P |
| 31 | 2 | 7 | Rhode Island (from Chappaqua) | Kei Igawa (prospect) |
P |
| 32 | 2 | 8 | San Diego | Jeff Samardzija (prospect) |
P |
| 33 | 2 | 9 | Jonesboro | Mike O'Connor | P |
| 34 | 2 | 10 | Chappaqua (from Stamford) | Endy Chavez | OF |
| 35 | 2 | 11 | Baton Rouge | Troy Cate (prospect) |
P |
| 36 | 2 | 12 | Arundel | Esteban German | 2B |
| 37 | 2 | 13 | Rhode Island | Josh Fields | 3B |
| 38 | 2 | 14 | Gulf Breeze | Ramon Ortiz | P |
| 39 | 2 | 15 | Green Bay | Eliezer Alfonzo | C |
| 40 | 2 | 16 | Freeport |
Cameron Maybin (prospect) |
OF |
| 41 | 2 | 17 | Tampa | Akinori Iwamura (prospect) |
3B |
| 42 | 2 | 18 | East Coast | Hong-chih Kuo | P |
| 43 | 2 | 19 | Turtle Beach | Evan Longoria (prospect) |
3B |
| 44 | 2 | 20 | Beantown | Fernando Nieve | P |
| 45 | 2 | 21 | Turtle Beach (from Glab) | Pat Neshek | P |
| 46 | 2 | 22 | Millers Tavern | Clayton Kershaw (prospect) |
P |
| 47 | 2 | 23 | Mokena | Mark Redman | P |
| 48 | 2 | 24 | Louisiana | Joe Saunders | P |
| Overall Pick |
Round number |
Pick number |
Player Selected | Pos | |
| 49 | 3 | 1 | Long Island | Scott Elbert (prospect) |
P |
| 50 | 3 | 2 | Greensboro | Jonathan Sanchez | P |
| 51 | 3 | 3 | Tidewater | Taylor Tankersley | P |
| 52 | 3 | 4 | Freeport (from Westchester) | Ryan Theriot | 2B |
| 53 | 3 | 5 | Texas | Jose Bautista | OF |
| 54 | 3 | 6 | Buffalo | Zach Miner | P |
| 55 | 3 | 7 | Chappaqua | Casey Janssen | P |
| 56 | 3 | 8 | San Diego | Joakim Soria (prospect) |
P |
| 57 | 3 | 9 | Buffalo (from Jonesboro) | Mike Thompson | P |
| 58 | 3 | 10 | Stamford | Cha Baek | P |
| 59 | 3 | 11 | Long Island (from Chappaqua through Baton Rouge) | Brian Bannister | P |
| 60 | 3 | 12 | Arundel | Scott Spiezio | 3B |
| 61 | 3 | 13 | Rhode Island | Hunter Pence (prospect) |
OF |
| 62 | 3 | 14 | Gulf Breeze | Darren Oliver | P |
| 63 | 3 | 15 | Green Bay | Scott Thorman | OF |
| 64 | 3 | 16 | Louisiana (from Freeport) | Luke Hochever (prospect) |
P |
| 65 | 3 | 17 | Tampa | Greg Norton | OF |
| 66 | 3 | 18 | Westchester (from East Coast) | Joey Votto (prospect) |
1B |
| 67 | 3 | 19 | Turtle Beach | Wil Ledezma | P |
| 68 | 3 | 20 | Beantown | Chris Coste | C |
| 69 | 3 | 21 | Glab | Chad Gaudin | P |
| 70 | 3 | 22 | Millers Tavern | Matt Albers | P |
| 71 | 3 | 23 | Louisiana (from Chappaqua through Mokena) | Chris Britton | P |
| 72 | 3 | 24 | Louisiana | Jose Tabata (prospect) |
OF |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 73 | 4 | 1 | Long Island | Cody Ross | OF |
| 74 | 4 | 2 | Greensboro | Ramon Ramirez | P |
| 75 | 4 | 3 | Tidewater | Joe Beimel | P |
| 76 | 4 | 4 | Westchester | Ryan Spilborghs | OF |
| 77 | 4 | 5 | Texas | Fernando
Martinez (prospect) |
OF |
| 78 | 4 | 6 | Freeport (from Buffalo) | Brian Sweeney | P |
| 79 | 4 | 7 | Chappaqua (from Mokena through Chappaqua) | Alan Embree | P |
| 80 | 4 | 8 | San Diego | Anthony Gwynn, Jr | OF |
| 81 | 4 | 9 | Jonesboro | Chad Paronto | P |
| 82 | 4 | 10 | Stamford | Alfredo Amezaga | OF |
| 83 | 4 | 11 | Baton Rouge | Colby Rasmus (prospect) |
OF |
| 84 | 4 | 12 | Arundel | Kevin Correia | P |
| 85 | 4 | 13 | Rhode Island | Carl Pavano (uncarded veteran) |
P |
| 86 | 4 | 14 | Gulf Breeze | Nick Adenhart (prospect) |
P |
| 87 | 4 | 15 | Green Bay | Kevin Frandsen | 2B |
| 88 | 4 | 16 | Freeport | Chris Sampson | P |
| 89 | 4 | 17 | Freeport (from Tampa) | Fabio Castro | P |
| 90 | 4 | 18 | East Coast | Andrew McCutchen (prospect) |
OF |
| 91 | 4 | 19 | East Coast (from Turtle Beach) | Carlos Gonzalez (prospect) |
OF |
| 92 | 4 | 20 | Beantown | Jeff Karsten | P |
| 93 | 4 | 21 | Glab | Jason Ellsbury (prospect) |
OF |
| 94 | 4 | 22 | East Coast (from Millers Tavern) | Kurt Suzuki (prospect) |
C |
| 95 | 4 | 23 | Westchester (from Mokena) | Collin Ballester (prospect) |
P |
| 96 | 4 | 24 | Louisiana | Darrell Rasner | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 97 | 5 | 1 | Long Island | Ben Zobrist | SS |
| 98 | 5 | 2 | Greensboro | Ruddy Lugo | P |
| 99 | 5 | 3 | Tidewater | Chuck Lofgren (prospect) |
P |
| 100 | 5 | 4 | Westchester | Carlos Gomez (prospect) |
OF |
| 101 | 5 | 5 | Texas | Steve Finley | OF |
| 102 | 5 | 6 | Buffalo | Jake Woods | P |
| 103 | 5 | 7 | East Coast (from Chappaqua) | Glen Perkins | P |
| 104 | 5 | 8 | San Diego | Rick Bauer | P |
| 105 | 5 | 9 | Jonesboro | Dave Borkowski | P |
| 106 | 5 | 10 | Freeport (from Chappaqua through Stamford) | Kory Casto (prospect) |
OF |
| 107 | 5 | 11 | Mokena (from Baton Rouge) | Joe Inglett | 2B |
| 108 | 5 | 12 | Arundel | Scott Cassidy | P |
| 109 | 5 | 13 | Rhode Island | Carlos Ruiz | C |
| 110 | 5 | 14 | Gulf Breeze | David Aardsma | P |
| 111 | 5 | 15 | Green Bay | Joe Koshansky (prospect) |
1B |
| 112 | 5 | 16 | Louisiana (from Freeport) | Josh Kinney | P |
| 113 | 5 | 17 | Tampa | Eric Gagne | P |
| 114 | 5 | 18 | East Coast | Jon Huber | P |
| 115 | 5 | 19 | Turtle Beach | Alexi Casilla | 2B |
| 116 | 5 | 20 | Beantown | Tim Corcoran | P |
| 117 | 5 | 21 | Glab | Tylor Yates | P |
| 118 | 5 | 22 | Millers Tavern | Alberto Callaspo | SS |
| 119 | 5 | 23 | Westchester (from Mokena) | C.J. Wilson | P |
| 120 | 5 | 24 | Louisiana | Kaz Matsui | 2B |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 121 | 6 | 1 | Long Island | Terrmel Sledge | OF |
| 122 | 6 | 2 | Greensboro | Clay Buchholz (prospect) |
P |
| 123 | 6 | 3 | Tidewater | Jose Garcia | P |
| 124 | 6 | 4 | Westchester | Bill Bray | P |
| 125 | 6 | 5 | Texas | Joe Randa | 3B |
| 126 | 6 | 6 | Buffalo | Brad Halsey | P |
| 127 | 6 | 7 | Chappaqua | Alex Escobar | OF |
| 128 | 6 | 8 | San Diego | Saul Rivera | P |
| 129 | 6 | 9 | Jonesboro | Brandon Fahey | OF |
| 130 | 6 | 10 | Stamford | Renyel Pinto | P |
| 131 | 6 | 11 | Baton Rouge | Sal Fasano | C |
| 132 | 6 | 12 | Arundel | Brandon Lyon | P |
| 133 | 6 | 13 | Rhode Island | John Koronka | P |
| 134 | 6 | 14 | Gulf Breeze | Macay McBride | P |
| 135 | 6 | 15 | Green Bay | Mike Rivera | C |
| 136 | 6 | 16 | Freeport | Jason Davis | P |
| 137 | 6 | 17 | Tampa | Alex Cora | SS |
| 138 | 6 | 18 | East Coast | Micah Bowie | P |
| 139 | 6 | 19 | Glab (from Turtle Beach) | Todd Wellemeyer | P |
| 140 | 6 | 20 | Beantown | Jason Grilli | P |
| 141 | 6 | 21 | Glab | Julio Franco | 1B |
| 142 | 6 | 22 | Millers Tavern | Jason Windsor | P |
| 143 | 6 | 23 | East Coast (from Mokena) | Shane Youman | P |
| 144 | 6 | 24 | Freeport (from Louisiana) | Eric Hurley (prospect) |
P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 145 | 7 | 1 | Long Island | Kyle Davies | P |
| 146 | 7 | 2 | Greensboro | Jorge Sosa | P |
| 147 | 7 | 3 | Tidewater | Edgar Gonzalez | P |
| 148 | 7 | 4 | Westchester | Rob Bowen | C |
| 149 | 7 | 5 | Texas | Anderson Hernandez | 2B |
| 150 | 7 | 6 | Buffalo | Jimmy Gobble | P |
| 151 | 7 | 7 | Mokena (from Chappaqua) | Ron Mahay | P |
| 152 | 7 | 8 | San Diego | Kevin Slowey (prospect) |
P |
| 153 | 7 | 9 | Jonesboro | Jason Tyner | OF |
| 154 | 7 | 10 | Turtle Beach (from Stamford) | Ron Flores | P |
| 155 | 7 | 11 | Baton Rouge | Tim Salmon | OF |
| 156 | 7 | 12 | Arundel | Bryan Corey | P |
| 157 | 7 | 13 | Rhode Island | Joaquin Arias | SS |
| 158 | 7 | 14 | Gulf Breeze | Josh Rupe | P |
| 159 | 7 | 15 | Green Bay | Travis Buck (prospect) |
OF |
| 160 | 7 | 16 | Freeport | Kason Gabbard | P |
| 161 | 7 | 17 | Tampa | Josh Paul | C |
| 162 | 7 | 18 | Turtle Beach (from East Coast) | Michael Bourn | OF |
| 163 | 7 | 19 | Turtle Beach | Eli Marrero | OF |
| 164 | 7 | 20 | Beantown | Scott Feldman | P |
| 165 | 7 | 21 | Glab | Brian Tallett | P |
| 166 | 7 | 22 | East Coast (from Millers Tavern) | Sammy Sosa (uncarded veteran) | OF |
| 167 | 7 | 23 | Beantown (from Mokena) | Koby Clemens (prospect) |
C |
| 168 | 7 | 24 | Louisiana | J.P. Howell | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 169 | 8 | 1 | Long Island | Elizardo Ramirez | P |
| 170 | 8 | 2 | Greensboro | Micah Owings (prospect) |
P |
| 171 | 8 | 3 | Tidewater | Seth McClung | P |
| 172 | 8 | 4 | Westchester | Brent Lillebridge (prospect) |
SS |
| 173 | 8 | 5 | Texas | Alay Soler | P |
| 174 | 8 | 6 | Buffalo | Scott Elarton | P |
| 175 | 8 | 7 | Stamford (from Chappaqua) | Humberto Sanchez (prospect) |
P |
| 176 | 8 | 8 | San Diego | Jose Hernandez | 1B |
| 177 | 8 | 9 | Jonesboro | Brayan Pena | C |
| 178 | 8 | 10 | Stamford | Troy Patton (prospect) |
P |
| 179 | 8 | 11 | Turtle Beach (from Baton Rouge) | J.D. Closser | C |
| 180 | 8 | 12 | Arundel | Manuel Corpas | P |
| 181 | 8 | 13 | Chappaqua (from Rhode Island) | Martin Prado | 2B |
| 182 | 8 | 14 | Gulf Breeze | Gary Bennett | C |
| 183 | 8 | 15 | Green Bay | Billy Traber | P |
| 184 | 8 | 16 | Mokena (from Freeport) | Dan Miceli | P |
| 185 | 8 | 17 | Tampa | Enrique Gonzalez | P |
| 186 | 8 | 18 | Chappaqua (from East Coast) | Donald Veal | P |
| 187 | 8 | 19 | Turtle Beach | Travis Snider (prospect) |
OF |
| 188 | 8 | 20 | Rhode Island (from Beantown) | Brandon Erbe (prospect) |
P |
| 189 | 8 | 21 | Glab | Brian Barton (prospect) |
OF |
| 190 | 8 | 22 | Arundel (from Millers Tavern) | Jacob McGee (prospect) |
P |
| 191 | 8 | 23 | Mokena | Charles Haeger | P |
| 192 | 8 | 24 | Louisiana | Anthony Lerew | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 193 | 9 | 1 | Long Island | Jae Seo | P |
| 194 | 9 | 2 | Greensboro | Daric Barton (prospect) |
1B |
| 195 | 9 | 3 | Tidewater | Shaun Marcum | P |
| 196 | 9 | 4 | Westchester | Devern Hansack | P |
| 197 | 9 | 5 | Texas | Curtis Thigpen (prospect) |
C |
| 198 | 9 | 6 | Buffalo | Paul Bako | C |
| 199 | 9 | 7 | East Coast (from Chappaqua) | Jeremy Affeldt | P |
| 200 | 9 | 8 | San Diego | Jason Hammel | P |
| 201 | 9 | 9 | Jonesboro | Will Startup (prospect) |
P |
| 202 | 9 | 10 | Stamford | Ubaldo Jimenez | P |
| 203 | 9 | 11 | Baton Rouge | Adam Melhuse | C |
| 204 | 9 | 12 | Arundel | David Price (prospect) |
P |
| 205 | 9 | 13 | Rhode Island | Octavio Dotel | P |
| 206 | 9 | 14 | Gulf Breeze | Elijah Dukes (prospect) |
OF |
| 207 | 9 | 15 | Green Bay | John Rheinecker | P |
| 208 | 9 | 16 | Freeport | Humberto Quintero | C |
| 209 | 9 | 17 | Tampa | Freddy Guzman | OF |
| 210 | 9 | 18 | East Coast | Marty McLeary | P |
| 211 | 9 | 19 | Stamford (from Turtle Beach) | Jeff Fiorentino | OF |
| 212 | 9 | 20 | Mokena (from Beantown) | Tyler Colvin (prospect) |
OF |
| 213 | 9 | 21 | Glab | Gabe Kapler | OF |
| 214 | 9 | 22 | Millers Tavern | Kyle Snyder | P |
| 215 | 9 | 23 | Mokena | Angel Pagan | OF |
| 216 | 9 | 24 | Louisiana | Joey Devine | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 217 | 10 | 1 | Long Island | Marlon Byrd | OF |
| 218 | 10 | 2 | Greensboro | Scott Schoeneweis | P |
| 219 | 10 | 3 | Tidewater | Trevor Crowe (prospect) |
OF |
| 220 | 10 | 4 | Westchester | Freddie Bynum | OF |
| 221 | 10 | 5 | Texas | Pass | |
| 222 | 10 | 6 | Buffalo | Sean Gallagher (prospect) |
P |
| 223 | 10 | 7 | Chappaqua | Yoshan Herrera (prospect) |
P |
| 224 | 10 | 8 | San Diego | Sean Camp | P |
| 225 | 10 | 9 | Jonesboro | Gary Majewski | P |
| 226 | 10 | 10 | Stamford | Todd Pratt | C |
| 227 | 10 | 11 | Baton Rouge | Jason Smith | 2B |
| 228 | 10 | 12 | Arundel | Alexis Gomez | OF |
| 229 | 10 | 13 | Rhode Island | Ken Ray | P |
| 230 | 10 | 14 | Gulf Breeze | Mark Lowe | P |
| 231 | 10 | 15 | Green Bay | Pass | |
| 232 | 10 | 16 | Freeport | Pass | |
| 233 | 10 | 17 | Tampa | John McDonald | SS |
| 234 | 10 | 18 | East Coast | Beltran Perez | P |
| 235 | 10 | 19 | Turtle Beach | Matt Smith | P |
| 236 | 10 | 20 | Mokena (from Beantown) | Aaron Guiel | OF |
| 237 | 10 | 21 | Glab | Matt Lindstrom (prospect) |
P |
| 238 | 10 | 22 | Millers Tavern | Jason Bergmann | P |
| 239 | 10 | 23 | Chappaqua (from Mokena) | Ross Ohlendorf (prospect) |
P |
| 240 | 10 | 24 | Louisiana | Sean Henn | P |
| Overall Pick |
Round number |
Pick number |
Team | Player Selected | Pos |
| 241 | 11 | 1 | Long Island | Will Inman (prospect) |
P |
| 242 | 11 | 2 | Greensboro | Todd Linden | OF |
| 243 | 11 | 3 | Tidewater | Jeremy Accardo | P |
| 244 | 11 | 4 | Westchester | Jeff Keppinger | 3B |
| 245 | 11 | 5 | Texas | Pass | |
| 246 | 11 | 6 | Buffalo | Billy Rowell (prospect) |
3B |
| 247 | 11 | 7 | Stamford (from Chappaqua) | Reggie Willits | OF |
| 248 | 11 | 8 | San Diego | Dexter Fowler (prospect) |
OF |
| 249 | 11 | 9 | Jonesboro | Tomas Perez | 3B |
| 250 | 11 | 10 | Stamford | Scott Moore | 1B |
| 251 | 11 | 11 | Baton Rouge | Miguel Cairo | 2B |
| 252 | 11 | 12 | Arundel | Sean West (prospect) |
P |
| 253 | 11 | 13 | Chappaqua (from Rhode Island) | Nick Massett | P |
| 254 | 11 | 14 | Gulf Breeze | John Mabry | 1B |
| 255 | 11 | 15 | Green Bay | Pass | |
| 256 | 11 | 16 | Freeport | Pass | |
| 257 | 11 | 17 | Tampa | Jeff Bailey (prospect) |
1B |
| 258 | 11 | 18 | East Coast | Pass | |
| 259 | 11 | 19 | Turtle Beach | Angel Sanchez | 2B |
| 260 | 11 | 20 | Mokena (from Beantown) | Brad Eldred (uncarded veteran) |
1B |
| 261 | 11 | 21 | Glab | Jason Botts | OF |
| 262 | 11 | 22 | Millers Tavern | Shawn Riggans | C |
| 263 | 11 | 23 | Mokena | Masumi Kuwata (prospect) |
P |
| 264 | 11 | 24 | Louisiana | Ryan Feierabend | P |
|
|
|
|
|
|
| XTR | 1 |