Held June 3 and 4, 2003
| Round | Pick | Player | Pos. | School | Hometown | Signed |
| 1 | 7 | Markakis, Nick | LHP/OF | Young Harris JC | , GA | |
| 2 | 44 | Finch, Brian | RHP | Texas A&M U | | |
| 3 | 74 | Ray, Christopher | RHP | College of William & Mary | | |
| 4 | 104 | McCrory, Robert | RHP | U. of Southern Mississippi | | |
| 5 | 134 | Spears, Nathaniel | SS | Charlotte HS | Port Charlotte, FL | |
| 6 | 164 | Sultemeier, Eric | CF | U. of Texas | | |
| 7 | 194 | Azze, Justin | LHP | U. of Hawaii | | |
| 8 | 224 | Nery, Nathan | LHP | Moon Area HS | Moon Area, PA | |
| 9 | 254 | Rine, Jarod | OF | West Virginia U. | | |
| 10 | 284 | Duncan, Jacob | OF | Texas Christian U. | | |
| 11 | 314 | Houston, Matt | C | Oklahoma City U. | | |
| 12 | 344 | Pulley, Matt | 3B | Woodland HS | Woodland, CA | |
| 13 | 374 | Hoey, James | RHP | Rider U. | | |
| 14 | 404 | Bock, Brian | C | U. of Hawaii | | |
| 15 | 434 | Timm, Jordan | LHP | U. of Wisconsin-Oskosh | | |
| 16 | 464 | Beck, Alan | OF | Western Carolina U. | | |
| 17 | 494 | Scott, Lorenzo | OF | Ball State U. | | |
| 18 | 524 | Furrow, Jason | LHP | Judson HS | Judson, TX | |
| 19 | 554 | Tolbert, Matt | 2B | U. of Mississippi | | |
| 20 | 584 | Neal, Tony | RHP | U. of South Alabama | | |
| 21 | 614 | Cash, David | SS | Northside Christian HS | St. Petersburg, FL | |
| 22 | 644 | Dixon, Zach | LHP | Texas A&M U | | |
| 23 | 674 | Wyrick, Dennis | 3B | Arizona State U. | | |
| 24 | 704 | McCurdy, Josh | OF | Niagara U. | | |
| 25 | 734 | Hummell, Richard | OF | Tombstone HS | Tombstone, AZ | |
| 26 | 764 | LeClerc, Brian | OF | Northside Christian HS | Clearwater, FL | |
| 27 | 794 | Brown, Travis | SS | Western Kentucky U. | | |
| 28 | 824 | Brocato, Russ | RHP | U. of Pennsylvania | | |
| 29 | 854 | Ward, Jason | RHP | Utah Valley State JC | | |
| 30 | 884 | Osentowski, Chris | RHP | Texas Christian U. | | |
| 31 | 914 | Brnardic, Ryan | RHP | Southeastern Oklahoma State U. | | |
| 32 | 944 | Wareham, Landon | 2B | Mesa State College | Olathe, CO | |
| 33 | 974 | Muyco, Jake | C | Columbia Basin CC | Richland, WA | |
| 34 | 1004 | Wiggins, Brad | OF | Howard CC | Fort Worth, TX | |
| 35 | 1034 | Orange, Richard | OF | Greenville HS | Greenville, TX | |
| 36 | 1064 | Martin, Danny | OF | Dunedin HS | Dunedin, FL | |
| 37 | 1094 | Smith, David | RHP | Chrysler HS | New Castle, IN | |
| 38 | 1124 | Garnett, Matthew | LHP | Stockdale HS | Bakersfield, CA | |
| 39 | 1154 | Corning, Shaun | LHP | Madison Area Technical College | | |
| 40 | 1184 | Welsh, Joe | LHP | Grand Rapids CC | | |
| 41 | 1214 | Feterl, Aaron | RHP | Crescenta Valley HS | La Crescenta, CA | |
| 42 | 1243 | Boudon, Chad | OF | U. of Washington | | |
| 43 | 1272 | George, Kyle | SS | U. of Maryland | | |
| 44 | 1300 | Houin, Scott | OF | Rampart HS | Colorado Springs, CO | |
| 45 | 1328 | Jensen, Brett | RHP | Iowa Central CC IA | | |
| 46 | 1355 | Young, Gregory | OF | Old Mill HS | Millersville, MD | |
| 47 | 1382 | Irle, Roy | RHP | Rend Lake (Ill.) JC IL | | |
| 48 | 1409 | McGuire, Cameron | C | McLennan CC | Grand Prairie, TX | |
| 49 | 1435 | Janssen, Casey | RHP | UCLA | | |
| 50 | 1461 | Ricciardulli, Adam | OF | Mission Bay HS | San Diego, CA | |