| 1 | 1 | June-Reg | Stephen Strasburg | RHP | 20 | 6-4 | 220 | R | R | College | | San Diego State University | $7,500,000 |
| 1 | 10 | June-Reg | Drew Storen | RHP | 21 | 6-2 | 180 | B | R | AA | | Stanford University | $1,600,000 |
| 2 | 50 | June-Reg | Jeff Kobernus | 2B | 21 | 6-2 | 195 | R | R | A- | | University of California | $705,000 |
| 3 | 81 | June-Reg | Trevor Holder | RHP | 22 | 6-2 | 185 | R | R | A+ | | University of Georgia | $200,000 |
| 4 | 112 | June-Reg | A.J. Morris | RHP | 22 | 6-2 | 176 | R | R | A | | Kansas State University | $270,000 |
| 5 | 142** | June-Reg | Miguel Pena | LHP | 18 | 6-2 | | L | L | - | | La Joya (La Joya,TX) | |
| 6 | 172 | June-Reg | Michael Taylor | SS | 18 | 6-2 | 190 | R | R | - | | Westminster Academy (Fort Lauderdale,FL) | $125,000 |
| 7 | 202 | June-Reg | Dean Weaver | RHP | 21 | 6-4 | 207 | R | R | A- | | University of Georgia | $124,500 |
| 8 | 232 | June-Reg | Roberto Perez | SS | 18 | 6-1 | 180 | R | R | Rookie | | | $150,000 |
| 9 | 262 | June-Reg | Taylor Jordan | RHP | 20 | 6-3 | 190 | R | R | Rookie | | Brevard College | $99,500 |
| 10 | 292 | June-Reg | Paul Applebee | LHP | 21 | 6-3 | 185 | L | L | A- | | University of California-Riverside | $95,000 |
| 11 | 322 | June-Reg | Justin Bloxom | LF | 21 | 6-1 | 196 | B | R | A- | | Kansas State University | |
| 12 | 352 | June-Reg | Nate Karns | RHP | 21 | 6-5 | 230 | R | R | College | | Texas Tech University | $225,000 |
| 13 | 382 | June-Reg | Pat Lehman | RHP | 22 | 6-4 | 215 | R | R | A | | George Washington University | |
| 14 | 412 | June-Reg | Naoya Washiya | RF | 20 | 5-11 | 175 | L | R | Rookie | | College of the Desert | |
| 15 | 442 | June-Reg | Corey Davis | 1B | 18 | 6-3 | 258 | R | R | - | | Coffee (Douglas,GA) | |
| 16 | 472 | June-Reg | Sean Nicol | SS | 22 | 5-11 | 170 | R | R | A- | | University of San Diego | |
| 17 | 502 | June-Reg | Chad Jenkins | LHP | 21 | 6-4 | 195 | L | L | A- | | Cecil College | $1,360,000 |
| 18 | 532 | June-Reg | Marcus Stroman | SS | 18 | 5-9 | 180 | R | R | - | | Patchogue-Medford (Patchogue,NY) | |
| 19 | 562 | June-Reg | Frank Corolla | RHP | 21 | 6-2 | 190 | R | R | College | | University of Houston | |
| 20 | 592 | June-Reg | Jake Walker | 3B | 22 | 6-3 | 220 | R | R | A- | | Concordia University | |
| 21 | 622 | June-Reg | Mitch Clegg | LHP | 22 | 6-4 | 222 | L | L | A- | | University of Massachusetts | |
| 22 | 652 | June-Reg | Danny Rosenbaum | LHP | 21 | 6-1 | 205 | R | L | Rookie | | Xavier University | |
| 23 | 682 | June-Reg | Kyle Breault | SS | 18 | 6-1 | 160 | R | R | Rookie | | Northville (Northville,MI) | |
| 24 | 712 | June-Reg | Dustin Crane | RHP | 22 | 6-0 | 175 | R | R | A- | | Snead State Community College | |
| 25 | 742 | June-Reg | Matt Ridings | RHP | 21 | | | | | College | | Western Kentucky University | |
| 26 | 772 | June-Reg | Gianison Boekhoudt | SS | 19 | 6-0 | 205 | L | R | - | | | |
| 27 | 802 | June-Reg | Brandon King | RHP | 18 | 6-4 | 240 | R | R | Rookie | | Martinsburg (Martinsburg,WV) | |
| 28 | 832 | June-Reg | Matt Swynenberg | RHP | 20 | 6-5 | 195 | R | R | A- | | Black Hawk College | |
| 29 | 862 | June-Reg | Evan Bronson | LHP | 22 | 6-3 | 195 | L | L | A- | | Trinity University | |
| 30 | 892 | June-Reg | Rob Wort | RHP | 20 | 6-2 | 170 | R | R | Rookie | | Jefferson College | |
| 31 | 922 | June-Reg | J.J. Sferra | CF | 23 | 5-11 | 160 | L | L | College | | UNLV | |
| 32 | 952 | June-Reg | Kyle Morrison | RHP | 21 | 6-1 | 190 | R | R | A- | | Wagner College | |
| 33 | 982 | June-Reg | Nicholas De Santiago | C | 18 | 6-0 | 210 | L | R | - | | Hays (Kyle,TX) | |
| 34 | 1012 | June-Reg | Shane Mccatty | RHP | 22 | 6-2 | 190 | R | R | Rookie | | Oakland University | |
| 35 | 1042 | June-Reg | Jacob Morris | CF | 18 | 6-3 | 195 | R | R | - | | Coppell (Coppell,TX) | |
| 36 | 1072 | June-Reg | Joshua Miller | LHP | 18 | 6-3 | 186 | L | L | - | | Sandra Day O'Connor (Helotes,TX) | |
| 37 | 1102 | June-Reg | Joshua Elander | C | 18 | 6-0 | 200 | R | R | - | | Round Rock (Round Rock,TX) | |
| 38 | 1132 | June-Reg | Christopher Manno | LHP | 20 | 6-2 | 170 | L | L | College | | Duke University | |
| 39 | 1162 | June-Reg | Kyle Martin | RHP | 18 | 6-6 | 195 | R | R | - | | | |
| 40 | 1192 | June-Reg | Joseph Hughes | RHP | 19 | 6-4 | | R | R | - | | McMichael (Mayodan,NC) | |
| 41 | 1222 | June-Reg | Dane Opel | CF | 18 | 6-2 | 193 | L | L | - | | Edwardsville (Edwardsville,IL) | |
| 42 | 1252 | June-Reg | Daniel Cropper | RHP | 21 | 6-4 | 200 | R | R | College | | University of North Carolina at Wilmington | |
| 43 | 1282 | June-Reg | Steven Walla | RHP | 18 | 6-4 | 170 | R | R | - | | Lake Travis (Austin,TX) | |
| 44 | 1312 | June-Reg | Hoby Milner | LHP | 18 | 6-3 | 165 | L | L | - | | Paschal (Fort Worth,TX) | |
| 45 | 1342 | June-Reg | Michael Ratterree | SS | 18 | 6-1 | | R | R | - | | | |
| 46 | 1372 | June-Reg | Seth Greene | RHP | 17 | 6-3 | 193 | R | R | - | | Deep Run (Glen Allen,VA) | |
| 47 | 1402 | June-Reg | Darius Rudoph | 2B | 20 | 5-11 | 190 | R | R | - | | Snead State Community College | |
| 48 | 1432 | June-Reg | Zach Dygert | C | 21 | 6-3 | 215 | R | R | College | | Ball State University | |
| 49 | 1462 | June-Reg | Jose Sermo | RF | 18 | 6-0 | 173 | S | R | - | | | |
| 50 | 1492 | June-Reg | Alvin Hines | CF | 18 | 6-0 | 195 | R | R | - | | Pelham (Pelham,AL) | |