| Week | Add | Drop |
| Week 1 |
SP John Burkett  | |
| Week 2 |
SP Jeff Fassero  | |
| Week 3 |
SP Chris Reitsma  |
SP Rob Bell |
| Week 4 |
RP Chris Michalak  |
SP Scott Williamson |
| Week 5 |
C Doug Mirabelli  |
OF Derek Bell  |
| Week 6 |
SP A.J. Burnett |
SP Steve Trachsel  |
| Week 7 |
1B Jeff Conine  |
C Doug Mirabelli  |
| Week 8 |
SS Frank Menechino  |
SP Jeff Fassero |
| Week 9 |
SP Roy Oswalt  |
2B Jose Ortiz SP Andy Benes  |
| Week 10 |
SP Charles Nagy  |
SP Chris Reitsma |
| Week 12 |
3B Travis Fryman | |
| Week 13 |
RP Odalis Perez |
SP Scott Elarton |
| Week 14 |
1B Kevin Young |
SP John Halama  |
| Week 16 |
SP Bud Smith |
RP Odalis Perez |
| 1st Team | 2nd Team | Votes |
| Week 12 | ||
| Magpies | Word 2 the Father | Decision |
|
SP
John Burkett
1B Jeff Conine 3B Scott Rolen  RP Chris Michalak SS Frank Menechino |
SP
Chan Ho Park
3B Jeff Cirillo  1B Richie Sexson  2B Jose Macias  RP Wade Miller |
Approved 16-1. See Breakdown |