Held June 7 and 8, 2004
| Round | Pick | Player | Pos. | School | Hometown | Signed |
|---|
| 1 | 8 | Townsend, Wade | RHP | Rice U | | |
| 3 | 79 | Fiorentino, Jeffrey | C | Florida Atlantic U. | | |
| 4 | 109 | Bergesen, Bradley | RHP | Foothill HS | | |
| 5 | 139 | Smith, Carl | LF | U. of Florida | | |
| 6 | 169 | Chamberlin, Bryce | RHP | Washington State U. | | |
| 7 | 199 | Johnston, John | SS | U. of Texas | | |
| 8 | 229 | Haehnel, David | LHP | U. of Illinois | | |
| 9 | 259 | Howell, Samuel | CF | Santaluces HS | | |
| 10 | 289 | Moffitt, Andrew | RF | Wichita State U. | | |
| 11 | 319 | Hart, Kevin | 1B | U. of Maryland | | |
| 12 | 349 | Puente, Juan | C | Bradley U. | | |
| 13 | 379 | Kitch, Denver | SS | Oklahoma City U. | | |
| 14 | 409 | Schmidt, Kyle | RHP | U. of South Florida | | |
| 15 | 439 | Venable, William | OF | Princeton U. | | |
| 16 | 469 | Schlindling, Andrew | RHP | St. Johns HS | | |
| 17 | 499 | Boehm, Kyle | RHP | Oakland U. | | |
| 18 | 529 | Baysinger, Trent | LHP | U. of Washington | | |
| 19 | 559 | McGuirk, Matthew | LF | Arlington Heights HS | | |
| 20 | 589 | Tucker, Jonathan | 2B | U. of Florida | | |
| 21 | 619 | Finan, Ryan | 1B | Lamar U. | | |
| 22 | 649 | Marconi, Robert | 3B | Northern Illinois U. | | |
| 23 | 679 | Schwabe, Ryan | LHP | U. of Louisiana | | |
| 24 | 709 | Mollenhauer, Dale | SS | Pine Richland HS | | |
| 25 | 739 | Minor, Zachary | LHP | Northern Illinois U. | | |
| 26 | 769 | Kotch, Kevin | C | Cecil CC | | |
| 27 | 799 | Wargo, Cody | C | Indiana U. | | |
| 28 | 829 | Graham, Alex | RHP | U. of the Pacific | | |
| 29 | 859 | Young, Marc | LHP | Riverside HS | | |
| 30 | 889 | Garcia, Jaime | LHP | Sharyland HS | | |
| 31 | 919 | Garnett, Matthew | LHP | Bakersfield CC | | |
| 32 | 949 | Jeffords, Raymond | RHP | Spartanburg Methodist Col | | |
| 33 | 979 | Elmore, Jared | RHP | Raymond HS | | |
| 34 | 1009 | Burns, Nicholas | C | Palomar Col. | | |
| 35 | 1039 | Crisp, Andrew | SS | Riverside HS | | |
| 36 | 1069 | Drewett, Jon | RHP | U. of Arkansas-Ft Smith JC | | |
| 37 | 1099 | Harrington, Ian | LHP | Bellevue CC | | |
| 38 | 1129 | Crisp, Adam | RF | Riverside HS | | |
| 39 | 1159 | Hill, Larry | LHP | Smithson Valley HS | | |
| 40 | 1189 | Roach, Jason | LHP | Sacramento CC | | |
| 41 | 1219 | Marinos, Demetrios | C | Steinhert HS | | |
| 42 | 1248 | Blackburn, Brian | C | Kellogg CC | | |
| 43 | 1277 | Casey, Bryan | C | Kofa HS | | |
| 44 | 1306 | Calderon, Leonardo | LHP | Puerto Rico BB Academy HS | | |
| 45 | 1335 | Basta, Samuel | LHP | Marquette HS | | |
| 46 | 1364 | Larson, Casey | RF | Paso Robles HS | | |
| 47 | 1393 | Daniels, Charles | RHP | Manteo HS | | |
| 48 | 1422 | Lane, Matthew | RHP | Iowa Western CC | | |
| 49 | 1450 | Turner, Clifton | RF | CCBC Catonsville | | |
| 50 | 1478 | Banks, Michael | RHP | Lake Michigan Col. | | |
