| East | W | L | Pct | GB |
| St. Louis | 101 | 61 | .623 | -- |
| NY Mets | 98 | 64 | .605 | 3.0 |
| Montreal | 84 | 77 | .522 | 16.5 |
| Chi Cubs | 77 | 84 | .478 | 23.5 |
| Philadelphia | 75 | 87 | .463 | 26.0 |
| Pittsburgh | 57 | 104 | .354 | 43.5 |
| Phase | Rnd | Ovl | Player | Pos | Current Status |
| Jan-Reg | 1 | 5 | Pat Gilbert | OF | Retired |
| Jan-Reg | 2 | 31 | Steve Taylor | OF | Retired |
| Jan-Reg | 3 | 57 | David Miller | P | Scout - Cleveland Indians (2013) |
| Jan-Reg | 4 | 83 | Mike Stevanus | SS | Retired |
| Jan-Reg | 5 | 109 | Troy Jackson | OF | Retired |
| Jan-Reg | 6 | 135 | Mitchell Ferrick | P | Retired |
| Jan-Reg | 7 | 160 | Barry Griffin | P | Retired |
| Jan-Reg | 8 | 184 | Craig Heakins | C | Retired |
| Jan-Reg | 9 | 208 | Derek Lee | 3B | Retired |
| Jan-Reg | 10 | 231 | James Warner | P | Inactive |
| Jan-Reg | 11 | 251 | Keith Swartzlander | P | Retired |
| Jan-Reg | 12 | 268 | Tom Hoffman | p | Inactive |
| Jan-Reg | 13 | 282 | John Vuz | C | Retired |
| Jan-Reg | 14 | 294 | Brian Warfel | OF | Retired |
| Jan-Sec | 1 | 19 | Greg Vaughn | OF | Retired |
| Jan-Sec | 2 | 45 | Ken Rahming | OF | Retired |
| Jan-Sec | 3 | 63 | Chris Ritter | P | Retired |
| June-Reg | 1 | 6 | Barry Bonds | OF | Retired |
| June-Reg | 2 | 47 | Damon Hansel | C | Retired |
| June-Reg | 3 | 60 | Joe Klancnik | P | Retired |
| June-Reg | 4 | 86 | Robin Vaughn | SS | Retired |
| June-Reg | 5 | 112 | Ondra Ford | OF | Retired |
| June-Reg | 6 | 138 | Brett Gideon | P | Retired |
| June-Reg | 7 | 164 | Tommy Gregg | OF | Hitting Coach - Omaha (2012) |
| June-Reg | 8 | 190 | Larry Melton | P | Retired |
| June-Reg | 9 | 216 | Terry Wakefield | OF | Retired |
| June-Reg | 10 | 242 | Jeff Cook | OF | Retired |
| June-Reg | 11 | 268 | Desmond Scieneaux | 1B | Retired |
| June-Reg | 12 | 294 | Bill Sampen | p | Retired |
| June-Reg | 13 | 320 | Brad Robinson | OF-1B | Retired |
| June-Reg | 14 | 346 | Kyle Todd | 3B | Retired |
| June-Reg | 15 | 372 | Luis Ramos | SS | Inactive |
| June-Reg | 16 | 398 | Ronnell Daniels | OF | Retired |
| June-Reg | 17 | 424 | Brian Zanardelli | p | Inactive |
| June-Reg | 18 | 450 | Juan McWilliams | 3B | Retired |
| June-Reg | 19 | 476 | Richard Kiluk | OF | Retired |
| June-Reg | 20 | 502 | John Shouse | C | Retired |
| June-Reg | 21 | 528 | Ray Gambino | SS | Retired |
| June-Reg | 22 | 554 | Mark Koller | p | Retired |
| June-Reg | 23 | 580 | Ralph Denkenberger | OF | Retired |
| June-Reg | 24 | 606 | Thomas Pierce | SS | Inactive |
| June-Reg | 25 | 632 | Bob Benkert | C | Retired |
| June-Reg | 26 | 658 | Mark Oberholtzer | p | Retired |
| June-Reg | 27 | 683 | Tony Mealy | OF | Retired |
| June-Reg | 28 | 708 | Kyle Channing | p | Retired |
| June-Reg | 29 | 730 | Lawrence Brady | OF | Retired |
| June-Reg | 30 | 751 | Brian Schaum | SS | Retired |
| June-Reg | 31 | 769 | Buster Lopes | p | Inactive |
| June-Reg | 32 | 783 | Greg Shirley | OF | Inactive |
| June-Reg | 33 | 797 | Scott Berry | OF | Retired |
| June-Reg | 34 | 809 | Page Odle | Of | Retired |
| June-Reg | 35 | 817 | Doug Smallwood | 3B | Retired |
| June-Reg | 36 | 822 | Tommy Shields | SS | Manager - Burlington (2013) |
| June-Sec | 1 | 4 | Tommy Hinzo | SS | Retired |
| June-Sec | 3 | 54 | Kirk Barry | OF | Retired |