| East | W | L | Pct | GB |
| Atlanta | 95 | 67 | .586 | -- |
| NY Mets | 94 | 68 | .580 | 1.0 |
| Florida | 79 | 82 | .491 | 15.5 |
| Montreal | 67 | 95 | .414 | 28.0 |
| Philadelphia | 65 | 97 | .401 | 30.0 |
| Phase | Rnd | Ovl | Player | Pos | Current Status |
| June-Reg | 1 | 29 | Adam Wainwright | P | STL 40m |
| June-Reg | 1 | 30 | Scott Thorman | IF | Inactive |
| June-Reg | 1 | 38 | Kelly Johnson | P | TB 40m |
| June-Reg | 1 | 40 | Aaron Herr | IF | Inactive |
| June-Reg | 2 | 51 | Bubba Nelson | P | Retired |
| June-Reg | 2 | 70 | Bryan Digby | P | Retired |
| June-Reg | 3 | 100 | Blaine Boyer | P | Free Agent |
| June-Reg | 4 | 106 | Zach Miner | P | PHI Minors [AAA] |
| June-Reg | 4 | 130 | Brian Montalbo | P | Retired |
| June-Reg | 5 | 160 | Chris Waters | P | Inactive |
| June-Reg | 6 | 190 | Matt Merricks | P | Retired |
| June-Reg | 7 | 220 | Brian Almeida | P | Retired |
| June-Reg | 8 | 250 | Robert Perkins | C | Retired |
| June-Reg | 9 | 280 | Ahmad Woods | OF | Retired |
| June-Reg | 10 | 310 | Rod Douglas | P | Retired |
| June-Reg | 11 | 340 | Kevin Cust | RF-C | Retired |
| June-Reg | 12 | 370 | Keoni DeRenne | ss | PIT Minors |
| June-Reg | 13 | 400 | Jonathan Rogers | P | Retired |
| June-Reg | 14 | 430 | Mike Machen | P | Retired |
| June-Reg | 15 | 460 | Armando Tejero | 1B | Retired |
| June-Reg | 16 | 490 | Andy Bent | P | Retired |
| June-Reg | 17 | 520 | Trey Hodges | P | Retired |
| June-Reg | 18 | 550 | Michael Davern | P | Retired |
| June-Reg | 19 | 580 | Charles Thomas | OF | KC Minors |
| June-Reg | 20 | 610 | Kyle Roat | C | Retired |
| June-Reg | 21 | 640 | Matt Wright | P | Free Agent |
| June-Reg | 22 | 670 | Josh Tillery | P | Retired |
| June-Reg | 23 | 700 | Mike Smalley | Retired | |
| June-Reg | 24 | 730 | Robert Moose | 1B | Retired |
| June-Reg | 25 | 760 | Tim McClendon | Retired | |
| June-Reg | 26 | 790 | Alph Coleman | LF | Retired |
| June-Reg | 27 | 820 | Joshua Wyrick | LF | Retired |
| June-Reg | 28 | 850 | Erick Contreras | SS | Retired |
| June-Reg | 29 | 880 | Adam LaRoche | 1B | WAN 40m |
| June-Reg | 30 | 910 | Quentin Jones | P | Retired |
| June-Reg | 31 | 940 | Delwyn Young | 2B | WAN Minors |
| June-Reg | 32 | 970 | Callix Crabbe | 2B | Inactive |
| June-Reg | 33 | 1000 | Tony Gwynn | OF | LAD Minors [AAA] |
| June-Reg | 34 | 1030 | Adam Brandenburg | P | Retired |
| June-Reg | 35 | 1060 | William Hall | P | Inactive |
| June-Reg | 36 | 1090 | Efren Lira | P | Retired |
| June-Reg | 37 | 1120 | Josh Parker | P | Retired |
| June-Reg | 38 | 1150 | Frank Arteaga | P | Retired |
| June-Reg | 39 | 1180 | Jimmy Rhodes | Retired | |
| June-Reg | 40 | 1209 | Adam Hilzendeger | P | Inactive |
| June-Reg | 41 | 1238 | Shane Hawk | P | Retired |
| June-Reg | 42 | 1267 | Zachariah Watson | P | Inactive |
| June-Reg | 43 | 1295 | Daniel Anderson | CF | Inactive |
| June-Reg | 44 | 1321 | Tanner Holecek | OF | Inactive |
| June-Reg | 45 | 1347 | Craig Bragg | CF | Inactive |
| June-Reg | 46 | 1371 | Brandon Green | Retired | |
| June-Reg | 47 | 1392 | Justin Bergh | P | Inactive |
| June-Reg | 48 | 1412 | Jason Herman | P | Inactive |
| June-Reg | 49 | 1432 | Bill Edwards | Retired | |
| June-Reg | 50 | 1452 | Drew Jackson | of | Retired |