| 2006-04-03 | vs CHN | 1 | L 7-16 | 0-1 | 5 | 42,591 | Aaron Harang | Carlos Zambrano | Will Ohman | Aaron Harang | | 7 | 16 | -9 |
| 2006-04-05 | vs CHN | 2 | W 8-6 | 1-1 | 5 | 27,287 | Bronson Arroyo | Glendon Rusch | Bronson Arroyo | Glendon Rusch | David Weathers | 15 | 22 | -7 |
| 2006-04-06 | vs PIT | 3 | W 6-5 | 2-1 | 3 | 13,887 | Brandon Claussen | Ian Snell | Rick White | Mike Gonzalez | David Weathers | 21 | 27 | -6 |
| 2006-04-07 | vs PIT | 4 | W 7-6 | 3-1 | 2 | 16,573 | Eric Milton | Paul Maholm | Eric Milton | Paul Maholm | Kent Mercker | 28 | 33 | -5 |
| 2006-04-08 | vs PIT | 5 | W 11-9 | 4-1 | 2 | 20,244 | Aaron Harang | Oliver Perez | Aaron Harang | Oliver Perez | Rick White | 39 | 42 | -3 |
| 2006-04-09 | vs PIT | 6 | L 3-5 | 4-2 | 3 | 22,090 | David Williams | Victor Santos | Victor Santos | David Williams | Roberto Hernandez | 42 | 47 | -5 |
| 2006-04-11 | @ CHN | 7 | W 9-2 | 5-2 | 1 | 36,708 | Bronson Arroyo | Glendon Rusch | Bronson Arroyo | Glendon Rusch | | 51 | 49 | 2 |
| 2006-04-12 | @ CHN | 8 | L 1-4 | 5-3 | 3 | 37,252 | Brandon Claussen | Greg Maddux | Greg Maddux | Brandon Claussen | Ryan Dempster | 52 | 53 | -1 |
| 2006-04-13 | @ CHN | 9 | W 8-3 | 6-3 | 1 | 40,881 | Eric Milton | Carlos Zambrano | Eric Milton | Carlos Zambrano | | 60 | 56 | 4 |
| 2006-04-14 | @ SLN | 10 | W 1-0 | 7-3 | 1 | 40,901 | Aaron Harang | Chris Carpenter | Aaron Harang | Chris Carpenter | David Weathers | 61 | 56 | 5 |
| 2006-04-15 | @ SLN | 11 | L 3-9 | 7-4 | 1 | 40,752 | David Williams | Sidney Ponson | Sidney Ponson | David Williams | | 64 | 65 | -1 |
| 2006-04-16 | @ SLN | 12 | L 7-8 | 7-5 | 3 | 40,068 | Bronson Arroyo | Mark Mulder | Braden Looper | David Weathers | | 71 | 73 | -2 |
| 2006-04-17 | vs FLO | 13 | W 9-1 | 8-5 | 3 | 16,960 | Brandon Claussen | Brian Moehler | Brandon Claussen | Brian Moehler | | 80 | 74 | 6 |
| 2006-04-18 | vs FLO | 14 | L 6-12 | 8-6 | 3 | 19,724 | Eric Milton | Jason Vargas | Josh Johnson | Eric Milton | | 86 | 86 | 0 |
| 2006-04-19 | vs FLO | 15 | W 9-8 | 9-6 | 3 | 18,881 | Aaron Harang | Dontrelle Willis | Todd Coffey | Todd Wellemeyer | | 95 | 94 | 1 |
| 2006-04-20 | @ MIL | 16 | W 12-8 | 10-6 | 3 | 15,347 | David Williams | Tomo Ohka | Matt Belisle | Justin Lehr | | 107 | 102 | 5 |
| 2006-04-21 | @ MIL | 17 | W 3-1 | 11-6 | 2 | 29,825 | Bronson Arroyo | Ben Sheets | Bronson Arroyo | Ben Sheets | David Weathers | 110 | 103 | 7 |
| 2006-04-22 | @ MIL | 18 | L 0-11 | 11-7 | 3 | 35,768 | Brandon Claussen | David Bush | David Bush | Brandon Claussen | | 110 | 114 | -4 |
| 2006-04-23 | @ MIL | 19 | W 11-0 | 12-7 | 2 | 29,174 | Aaron Harang | Doug Davis | Aaron Harang | Doug Davis | | 121 | 114 | 7 |
| 2006-04-24 | @ WAS | 20 | W 4-2 | 13-7 | 2 | 19,264 | Elizardo Ramirez | Livan Hernandez | Elizardo Ramirez | Livan Hernandez | David Weathers | 125 | 116 | 9 |
| 2006-04-25 | @ WAS | 21 | W 6-5 | 14-7 | 2 | 21,642 | David Williams | Billy Traber | David Williams | Billy Traber | David Weathers | 131 | 121 | 10 |
| 2006-04-26 | @ WAS | 22 | W 5-0 | 15-7 | 2 | 19,380 | Bronson Arroyo | Ramon Ortiz | Bronson Arroyo | Ramon Ortiz | | 136 | 121 | 15 |
| 2006-04-28 | vs HOU | 23 | W 5-4 | 16-7 | 1 | 32,089 | Brandon Claussen | Roy Oswalt | Brandon Claussen | Roy Oswalt | David Weathers | 141 | 125 | 16 |
| 2006-04-29 | vs HOU | 24 | W 6-3 | 17-7 | 1 | 24,873 | Aaron Harang | Andy Pettitte | Aaron Harang | Andy Pettitte | David Weathers | 147 | 128 | 19 |
| 2006-04-30 | vs HOU | 25 | L 2-3 | 17-8 | 1 | 22,814 | Elizardo Ramirez | Taylor Buchholz | Taylor Buchholz | Elizardo Ramirez | Brad Lidge | 149 | 131 | 18 |
| 2006-05-01 | vs SLN | 26 | W 6-1 | 18-8 | 1 | 20,900 | Bronson Arroyo | Mark Mulder | Bronson Arroyo | Mark Mulder | | 155 | 132 | 23 |
| 2006-05-02 | vs SLN | 27 | W 3-2 | 19-8 | 1 | 25,127 | David Williams | Sidney Ponson | Todd Coffey | Brian Falkenborg | | 158 | 134 | 24 |
| 2006-05-03 | @ COL | 28 | L 0-3 | 19-9 | 1 | 18,214 | Brandon Claussen | Jeff Francis | Jeff Francis | Brandon Claussen | Brian Fuentes | 158 | 137 | 21 |
| 2006-05-04 | @ COL | 29 | W 7-1 | 20-9 | 1 | 18,204 | Aaron Harang | Josh Fogg | Aaron Harang | Josh Fogg | | 165 | 138 | 27 |
| 2006-05-05 | @ ARI | 30 | L 1-7 | 20-10 | 1 | 21,072 | Elizardo Ramirez | Brandon Webb | Brandon Webb | Elizardo Ramirez | | 166 | 145 | 21 |
| 2006-05-06 | @ ARI | 31 | L 1-3 | 20-11 | 1 | 27,398 | Bronson Arroyo | Claudio Vargas | Claudio Vargas | Bronson Arroyo | Jose Valverde | 167 | 148 | 19 |
| 2006-05-07 | @ ARI | 32 | W 9-8 | 21-11 | 1 | 27,707 | David Williams | Orlando Hernandez | David Williams | Orlando Hernandez | David Weathers | 176 | 156 | 20 |
| 2006-05-09 | vs WAS | 33 | L 1-7 | 21-12 | 1 | 16,716 | Brandon Claussen | Tony Armas | Tony Armas | Brandon Claussen | | 177 | 163 | 14 |
| 2006-05-10 | vs WAS | 34 | W 9-6 | 22-12 | 1 | 14,180 | Aaron Harang | Livan Hernandez | David Weathers | Mike Stanton | | 186 | 169 | 17 |
| 2006-05-11 | vs WAS | 35 | W 5-4 | 23-12 | 1 | 15,771 | Bronson Arroyo | Zach Day | Brian Shackelford | Joey Eischen | | 191 | 173 | 18 |
| 2006-05-12 | vs PHI | 36 | L 4-8 | 23-13 | 1 | 21,709 | Elizardo Ramirez | Cole Hamels | Ryan Madson | Elizardo Ramirez | Tom Gordon | 195 | 181 | 14 |
| 2006-05-13 | vs PHI | 37 | L 0-2 | 23-14 | 2 | 32,620 | David Williams | Jon Lieber | Jon Lieber | David Williams | Tom Gordon | 195 | 183 | 12 |
| 2006-05-14 | vs PHI | 38 | L 1-2 | 23-15 | 2 | 19,673 | Brandon Claussen | Brett Myers | Geoff Geary | Chris Hammond | Tom Gordon | 196 | 185 | 11 |
| 2006-05-16 | @ PIT | 39 | L 3-9 | 23-16 | 2 | 14,315 | Aaron Harang | Paul Maholm | Paul Maholm | Aaron Harang | | 199 | 194 | 5 |
| 2006-05-17 | @ PIT | 40 | L 2-7 | 23-17 | 2 | 14,897 | Bronson Arroyo | Oliver Perez | Oliver Perez | Bronson Arroyo | | 201 | 201 | 0 |
| 2006-05-18 | @ PIT | 41 | W 9-8 | 24-17 | 2 | 18,502 | David Williams | Victor Santos | Matt Belisle | Matt Capps | Todd Coffey | 210 | 209 | 1 |
| 2006-05-19 | @ DET | 42 | W 9-4 | 25-17 | 2 | 26,933 | Brandon Claussen | Jeremy Bonderman | Brandon Claussen | Jeremy Bonderman | | 219 | 213 | 6 |
| 2006-05-20 | @ DET | 43 | L 6-7 | 25-18 | 2 | 43,128 | Eric Milton | Mike Maroth | Fernando Rodney | David Weathers | | 225 | 220 | 5 |
| 2006-05-21 | @ DET | 44 | L 0-1 | 25-19 | 2 | 31,515 | Aaron Harang | Nate Robertson | Fernando Rodney | Aaron Harang | Todd Jones | 225 | 221 | 4 |
| 2006-05-22 | vs MIL | 45 | W 15-5 | 26-19 | 2 | 16,567 | Bronson Arroyo | David Bush | Bronson Arroyo | David Bush | | 240 | 226 | 14 |
| 2006-05-23 | vs MIL | 46 | W 7-3 | 27-19 | 2 | 16,528 | Elizardo Ramirez | Dana Eveland | Elizardo Ramirez | Dana Eveland | | 247 | 229 | 18 |
| 2006-05-24 | vs MIL | 47 | L 2-6 | 27-20 | 2 | 29,065 | Brandon Claussen | Doug Davis | Doug Davis | Brandon Claussen | | 249 | 235 | 14 |
| 2006-05-26 | vs ARI | 48 | L 0-3 | 27-21 | 2 | 33,751 | Eric Milton | Brandon Webb | Brandon Webb | Eric Milton | | 249 | 238 | 11 |
| 2006-05-27 | vs ARI | 49 | L 0-7 | 27-22 | 2 | 36,884 | Aaron Harang | Juan Cruz | Juan Cruz | Aaron Harang | | 249 | 245 | 4 |
| 2006-05-28 | vs ARI | 50 | W 5-4 | 28-22 | 2 | 27,694 | Bronson Arroyo | Enrique Gonzalez | David Weathers | Jose Valverde | | 254 | 249 | 5 |
| 2006-05-29 | @ CHN | 51 | L 3-7 | 28-23 | 2 | 40,072 | Elizardo Ramirez | Kerry Wood | Kerry Wood | Elizardo Ramirez | Ryan Dempster | 257 | 256 | 1 |
| 2006-05-30 | @ CHN | 52 | L 3-8 | 28-24 | 2 | 39,000 | Brandon Claussen | Greg Maddux | Greg Maddux | Brandon Claussen | | 260 | 264 | -4 |
| 2006-05-31 | @ CHN | 53 | W 3-2 | 29-24 | 2 | 39,810 | Eric Milton | Carlos Zambrano | Eric Milton | Carlos Zambrano | Todd Coffey | 263 | 266 | -3 |
| 2006-06-02 | @ HOU | 54 | W 14-3 | 30-24 | 2 | 37,086 | Aaron Harang | Wandy Rodriguez | Aaron Harang | Wandy Rodriguez | | 277 | 269 | 8 |
| 2006-06-03 | @ HOU | 55 | W 7-5 | 31-24 | 2 | 39,653 | Bronson Arroyo | Andy Pettitte | Bronson Arroyo | Andy Pettitte | | 284 | 274 | 10 |
| 2006-06-04 | @ HOU | 56 | W 6-4 | 32-24 | 2 | 37,532 | Elizardo Ramirez | Fernando Nieve | Todd Coffey | Dan Wheeler | Esteban Yan | 290 | 278 | 12 |
| 2006-06-05 | @ SLN | 57 | W 8-7 | 33-24 | 2 | 43,707 | Brandon Claussen | Jeff Suppan | Esteban Yan | Jason Isringhausen | Todd Coffey | 298 | 285 | 13 |
| 2006-06-06 | @ SLN | 58 | W 7-0 | 34-24 | 2 | 43,857 | Eric Milton | Chris Carpenter | Eric Milton | Chris Carpenter | | 305 | 285 | 20 |
| 2006-06-07 | @ SLN | 59 | W 7-4 | 35-24 | 1 | 44,306 | Aaron Harang | Sidney Ponson | Aaron Harang | Sidney Ponson | Todd Coffey | 312 | 289 | 23 |
| 2006-06-08 | vs CHN | 60 | W 7-1 | 36-24 | 1 | 26,059 | Bronson Arroyo | Glendon Rusch | Bronson Arroyo | Glendon Rusch | | 319 | 290 | 29 |
| 2006-06-09 | vs CHN | 61 | L 5-6 | 36-25 | 2 | 41,064 | Elizardo Ramirez | Greg Maddux | Greg Maddux | Elizardo Ramirez | Ryan Dempster | 324 | 296 | 28 |
| 2006-06-10 | vs CHN | 62 | L 2-4 | 36-26 | 2 | 34,141 | Brandon Claussen | Carlos Zambrano | Carlos Zambrano | Brandon Claussen | Ryan Dempster | 326 | 300 | 26 |
| 2006-06-11 | vs CHN | 63 | L 3-9 | 36-27 | 2 | 27,250 | Eric Milton | Carlos Marmol | Carlos Marmol | Eric Milton | | 329 | 309 | 20 |
| 2006-06-12 | vs MIL | 64 | L 5-6 | 36-28 | 2 | 19,279 | Aaron Harang | Zach Jackson | Zach Jackson | Kent Mercker | Derrick Turnbow | 334 | 315 | 19 |
| 2006-06-13 | vs MIL | 65 | L 4-6 | 36-29 | 2 | 21,829 | Bronson Arroyo | Doug Davis | Doug Davis | Bronson Arroyo | Derrick Turnbow | 338 | 321 | 17 |
| 2006-06-14 | vs MIL | 66 | W 3-0 | 37-29 | 2 | 27,716 | Elizardo Ramirez | Carlos Villanueva | Chris Hammond | Danny Kolb | | 341 | 321 | 20 |
| 2006-06-16 | vs CHA | 67 | L 4-12 | 37-30 | 2 | 32,673 | Brandon Claussen | Freddy Garcia | Freddy Garcia | Brandon Claussen | | 345 | 333 | 12 |
| 2006-06-17 | vs CHA | 68 | L 6-8 | 37-31 | 2 | 39,451 | Eric Milton | Jose Contreras | Matt Thornton | Todd Coffey | Bobby Jenks | 351 | 341 | 10 |
| 2006-06-18 | vs CHA | 69 | L 1-8 | 37-32 | 2 | 31,569 | Aaron Harang | Jon Garland | Jon Garland | Aaron Harang | | 352 | 349 | 3 |
| 2006-06-19 | @ NYN | 70 | W 4-2 | 38-32 | 2 | 41,874 | Bronson Arroyo | Orlando Hernandez | Bronson Arroyo | Orlando Hernandez | | 356 | 351 | 5 |
| 2006-06-20 | @ NYN | 71 | L 2-9 | 38-33 | 2 | 38,991 | Elizardo Ramirez | Steve Trachsel | Steve Trachsel | Elizardo Ramirez | | 358 | 360 | -2 |
| 2006-06-21 | @ NYN | 72 | W 6-5 | 39-33 | 2 | 49,758 | Joe Mays | Alay Soler | Jason Standridge | Billy Wagner | Todd Coffey | 364 | 365 | -1 |
| 2006-06-22 | @ NYN | 73 | L 2-6 | 39-34 | 2 | 46,767 | Eric Milton | Pedro Martinez | Pedro Martinez | Eric Milton | Chad Bradford | 366 | 371 | -5 |
| 2006-06-23 | @ CLE | 74 | W 3-0 | 40-34 | 2 | 32,927 | Aaron Harang | Jake Westbrook | Aaron Harang | Jake Westbrook | | 369 | 371 | -2 |
| 2006-06-24 | @ CLE | 75 | L 0-4 | 40-35 | 2 | 33,072 | Bronson Arroyo | Paul Byrd | Paul Byrd | Bronson Arroyo | | 369 | 375 | -6 |
| 2006-06-25 | @ CLE | 76 | W 4-2 | 41-35 | 2 | 33,139 | Elizardo Ramirez | Jeremy Sowers | Elizardo Ramirez | Jeremy Sowers | Todd Coffey | 373 | 377 | -4 |
| 2006-06-27 | vs KCA | 77 | L 8-9 | 41-36 | 2 | 21,420 | Eric Milton | Mike Wood | Jeremy Affeldt | Todd Coffey | Ambiorix Burgos | 381 | 386 | -5 |
| 2006-06-28 | vs KCA | 78 | W 7-2 | 42-36 | 2 | 34,648 | Aaron Harang | Scott Elarton | Aaron Harang | Scott Elarton | | 388 | 388 | 0 |
| 2006-06-29 | vs KCA | 79 | W 6-5 | 43-36 | 2 | 22,093 | Bronson Arroyo | Bobby Keppel | David Weathers | Elmer Dessens | Todd Coffey | 394 | 393 | 1 |
| 2006-06-30 | vs CLE | 80 | W 9-8 | 44-36 | 2 | 34,930 | Elizardo Ramirez | Paul Byrd | Kent Mercker | Bob Wickman | | 403 | 401 | 2 |
| 2006-07-01 | vs CLE | 81 | L 7-12 | 44-37 | 2 | 40,692 | Joe Mays | Cliff Lee | Cliff Lee | Joe Mays | | 410 | 413 | -3 |
| 2006-07-02 | vs CLE | 82 | L 3-6 | 44-38 | 2 | 36,849 | Eric Milton | CC Sabathia | Guillermo Mota | David Weathers | Bob Wickman | 413 | 419 | -6 |
| 2006-07-03 | @ MIL | 83 | L 7-8 | 44-39 | 2 | 31,353 | Aaron Harang | David Bush | Matt Wise | Todd Coffey | | 420 | 427 | -7 |
| 2006-07-04 | @ MIL | 84 | L 2-5 | 44-40 | 2 | 39,280 | Bronson Arroyo | Doug Davis | Doug Davis | Bronson Arroyo | Brian Shouse | 422 | 432 | -10 |
| 2006-07-05 | @ MIL | 85 | L 5-6 | 44-41 | 2 | 19,651 | Elizardo Ramirez | Carlos Villanueva | Geremi Gonzalez | Jason Standridge | | 427 | 438 | -11 |
| 2006-07-06 | @ ATL | 86 | L 7-8 | 44-42 | 2 | 28,446 | Joe Mays | Tim Hudson | Ken Ray | Todd Coffey | | 434 | 446 | -12 |
| 2006-07-07 | @ ATL | 87 | W 10-5 | 45-42 | 2 | 32,315 | Eric Milton | Horacio Ramirez | Eric Milton | Horacio Ramirez | | 444 | 451 | -7 |
| 2006-07-08 | @ ATL | 88 | L 1-4 | 45-43 | 2 | 44,718 | Aaron Harang | John Smoltz | John Smoltz | Aaron Harang | Ken Ray | 445 | 455 | -10 |
| 2006-07-09 | @ ATL | 89 | L 3-8 | 45-44 | 2 | 31,908 | Bronson Arroyo | John Thomson | Oscar Villarreal | Bronson Arroyo | | 448 | 463 | -15 |
| 2006-07-13 | vs COL | 90 | W 9-7 | 46-44 | 2 | 20,660 | Eric Milton | Jeff Francis | Eric Milton | Jeff Francis | Eddie Guardado | 457 | 470 | -13 |
| 2006-07-14 | vs COL | 91 | W 3-1 | 47-44 | 2 | 22,497 | Aaron Harang | Jason Jennings | Aaron Harang | Jason Jennings | Eddie Guardado | 460 | 471 | -11 |
| 2006-07-15 | vs COL | 92 | W 3-2 | 48-44 | 2 | 35,396 | Bronson Arroyo | Aaron Cook | Bill Bray | Brian Fuentes | | 463 | 473 | -10 |
| 2006-07-16 | vs COL | 93 | W 6-4 | 49-44 | 2 | 27,043 | Elizardo Ramirez | Josh Fogg | Todd Coffey | Jose Mesa | Eddie Guardado | 469 | 477 | -8 |
| 2006-07-18 | vs NYN | 94 | L 3-8 | 49-45 | 2 | 27,138 | Eric Milton | Mike Pelfrey | Mike Pelfrey | Eric Milton | | 472 | 485 | -13 |
| 2006-07-19 | vs NYN | 95 | W 7-4 | 50-45 | 2 | 26,300 | Aaron Harang | Steve Trachsel | Todd Coffey | Duaner Sanchez | Eddie Guardado | 479 | 489 | -10 |
| 2006-07-20 | vs NYN | 96 | L 2-4 | 50-46 | 2 | 28,729 | Bronson Arroyo | Tom Glavine | Pedro Feliciano | Gary Majewski | Billy Wagner | 481 | 493 | -12 |
| 2006-07-21 | vs MIL | 97 | W 6-5 | 51-46 | 2 | 19,677 | Elizardo Ramirez | Chris Capuano | Gary Majewski | Derrick Turnbow | | 487 | 498 | -11 |
| 2006-07-22 | vs MIL | 98 | W 8-7 | 52-46 | 2 | 41,915 | Joe Mays | David Bush | Todd Coffey | Geremi Gonzalez | Eddie Guardado | 495 | 505 | -10 |
| 2006-07-23 | vs MIL | 99 | L 1-4 | 52-47 | 2 | 22,726 | Eric Milton | Tomo Ohka | Tomo Ohka | Eric Milton | Danny Kolb | 496 | 509 | -13 |
| 2006-07-25 | @ HOU | 100 | W 2-0 | 53-47 | 2 | 38,865 | Aaron Harang | Roger Clemens | Aaron Harang | Roger Clemens | Bill Bray | 498 | 509 | -11 |
| 2006-07-26 | @ HOU | 101 | L 5-8 | 53-48 | 2 | 34,381 | Bronson Arroyo | Andy Pettitte | Andy Pettitte | Bronson Arroyo | Dan Wheeler | 503 | 517 | -14 |
| 2006-07-27 | @ HOU | 102 | W 8-4 | 54-48 | 2 | 38,254 | Elizardo Ramirez | Taylor Buchholz | Elizardo Ramirez | Taylor Buchholz | | 511 | 521 | -10 |
| 2006-07-28 | @ MIL | 103 | W 4-3 | 55-48 | 2 | 32,743 | Eric Milton | Tomo Ohka | Eric Milton | Matt Wise | Eddie Guardado | 515 | 524 | -9 |
| 2006-07-29 | @ MIL | 104 | L 3-6 | 55-49 | 2 | 43,000 | Justin Germano | Doug Davis | Geremi Gonzalez | Justin Germano | Derrick Turnbow | 518 | 530 | -12 |
| 2006-07-30 | @ MIL | 105 | L 3-4 | 55-50 | 2 | 42,976 | Aaron Harang | Ben Sheets | Ben Sheets | Aaron Harang | Francisco Cordero | 521 | 534 | -13 |
| 2006-08-01 | vs LAN | 106 | L 4-10 | 55-51 | 2 | 25,127 | Bronson Arroyo | Aaron Sele | Aaron Sele | Bill Bray | | 525 | 544 | -19 |
| 2006-08-02 | vs LAN | 107 | L 3-5 | 55-52 | 2 | 22,110 | Elizardo Ramirez | Brad Penny | Brad Penny | Elizardo Ramirez | Takashi Saito | 528 | 549 | -21 |
| 2006-08-03 | vs LAN | 108 | L 0-3 | 55-53 | 2 | 26,053 | Eric Milton | Greg Maddux | Greg Maddux | Eric Milton | Takashi Saito | 528 | 552 | -24 |
| 2006-08-04 | vs ATL | 109 | W 5-4 | 56-53 | 2 | 33,661 | Aaron Harang | Chuck James | Aaron Harang | Chuck James | Eddie Guardado | 533 | 556 | -23 |
| 2006-08-05 | vs ATL | 110 | W 8-6 | 57-53 | 2 | 33,170 | Bronson Arroyo | Jason Shiell | David Weathers | Tyler Yates | Bill Bray | 541 | 562 | -21 |
| 2006-08-06 | vs ATL | 111 | L 4-6 | 57-54 | 2 | 29,660 | Kyle Lohse | John Smoltz | Macay McBride | Gary Majewski | Bob Wickman | 545 | 568 | -23 |
| 2006-08-07 | vs SLN | 112 | L 1-13 | 57-55 | 2 | 34,262 | Elizardo Ramirez | Jeff Weaver | Jeff Weaver | Elizardo Ramirez | | 546 | 581 | -35 |
| 2006-08-08 | vs SLN | 113 | W 10-3 | 58-55 | 2 | 40,094 | Eric Milton | Jason Marquis | Eric Milton | Jason Marquis | | 556 | 584 | -28 |
| 2006-08-09 | vs SLN | 114 | W 8-7 | 59-55 | 2 | 41,649 | Aaron Harang | Chris Carpenter | Ryan Franklin | Jason Isringhausen | | 564 | 591 | -27 |
| 2006-08-10 | vs SLN | 115 | L 1-6 | 59-56 | 2 | 39,591 | Bronson Arroyo | Anthony Reyes | Anthony Reyes | Bronson Arroyo | | 565 | 597 | -32 |
| 2006-08-11 | @ PHI | 116 | L 5-6 | 59-57 | 2 | 41,461 | Kyle Lohse | Jon Lieber | Aaron Fultz | Elizardo Ramirez | | 570 | 603 | -33 |
| 2006-08-12 | @ PHI | 117 | W 9-7 | 60-57 | 2 | 39,553 | Elizardo Ramirez | Scott Mathieson | Chris Michalak | Tom Gordon | Eddie Guardado | 579 | 610 | -31 |
| 2006-08-13 | @ PHI | 118 | W 7-5 | 61-57 | 2 | 37,677 | Eric Milton | Brett Myers | Bill Bray | Ryan Madson | | 586 | 615 | -29 |
| 2006-08-15 | @ SLN | 119 | L 0-5 | 61-58 | 2 | 42,761 | Aaron Harang | Chris Carpenter | Chris Carpenter | Aaron Harang | | 586 | 620 | -34 |
| 2006-08-16 | @ SLN | 120 | W 7-2 | 62-58 | 2 | 42,752 | Bronson Arroyo | Anthony Reyes | Bronson Arroyo | Anthony Reyes | | 593 | 622 | -29 |
| 2006-08-17 | @ SLN | 121 | L 1-2 | 62-59 | 2 | 40,346 | Kyle Lohse | Jeff Weaver | Jason Isringhausen | Ryan Franklin | | 594 | 624 | -30 |
| 2006-08-18 | vs PIT | 122 | L 3-7 | 62-60 | 2 | 31,718 | Chris Michalak | Ian Snell | Ian Snell | Chris Michalak | | 597 | 631 | -34 |
| 2006-08-19 | vs PIT | 123 | W 14-7 | 63-60 | 2 | 34,245 | Eric Milton | Paul Maholm | Ryan Franklin | Salomon Torres | | 611 | 638 | -27 |
| 2006-08-20 | vs PIT | 124 | W 5-1 | 64-60 | 2 | 29,935 | Aaron Harang | Victor Santos | Aaron Harang | Victor Santos | | 616 | 639 | -23 |
| 2006-08-21 | vs HOU | 125 | W 4-3 | 65-60 | 2 | 24,110 | Bronson Arroyo | Andy Pettitte | Ryan Franklin | Chad Qualls | Scott Schoeneweis | 620 | 642 | -22 |
| 2006-08-22 | vs HOU | 126 | W 14-0 | 66-60 | 2 | 22,556 | Kyle Lohse | Jason Hirsh | Kyle Lohse | Jason Hirsh | | 634 | 642 | -8 |
| 2006-08-23 | vs HOU | 127 | L 3-7 | 66-61 | 2 | 24,873 | Chris Michalak | Roy Oswalt | Roy Oswalt | Todd Coffey | | 637 | 649 | -12 |
| 2006-08-24 | @ SFN | 128 | W 6-3 | 67-61 | 2 | 38,754 | Eric Milton | Brad Hennessey | Ryan Franklin | Vinnie Chulk | David Weathers | 643 | 652 | -9 |
| 2006-08-25 | @ SFN | 129 | L 1-4 | 67-62 | 2 | 37,801 | Aaron Harang | Matt Morris | Matt Morris | Aaron Harang | | 644 | 656 | -12 |
| 2006-08-26 | @ SFN | 130 | L 1-4 | 67-63 | 2 | 41,362 | Bronson Arroyo | Noah Lowry | Noah Lowry | Bronson Arroyo | Mike Stanton | 645 | 660 | -15 |
| 2006-08-27 | @ SFN | 131 | L 0-8 | 67-64 | 2 | 39,097 | Kyle Lohse | Matt Cain | Matt Cain | Kyle Lohse | | 645 | 668 | -23 |
| 2006-08-28 | @ LAN | 132 | L 5-6 | 67-65 | 2 | 44,176 | Chris Michalak | Brad Penny | Brad Penny | Chris Michalak | Jonathan Broxton | 650 | 674 | -24 |
| 2006-08-29 | @ LAN | 133 | L 5-6 | 67-66 | 2 | 44,697 | Eric Milton | Mark Hendrickson | Derek Lowe | Ryan Franklin | | 655 | 680 | -25 |
| 2006-08-30 | @ LAN | 134 | L 3-7 | 67-67 | 2 | 47,356 | Aaron Harang | Greg Maddux | Greg Maddux | Aaron Harang | | 658 | 687 | -29 |
| 2006-09-01 | @ SDN | 135 | W 6-2 | 68-67 | 2 | 32,901 | Bronson Arroyo | Clay Hensley | Bronson Arroyo | Clay Hensley | | 664 | 689 | -25 |
| 2006-09-02 | @ SDN | 136 | L 1-7 | 68-68 | 2 | 36,287 | Kyle Lohse | Jake Peavy | Jake Peavy | Kyle Lohse | | 665 | 696 | -31 |
| 2006-09-03 | @ SDN | 137 | L 1-2 | 68-69 | 2 | 31,153 | Eric Milton | David Wells | Cla Meredith | Rheal Cormier | Trevor Hoffman | 666 | 698 | -32 |
| 2006-09-04 | vs SFN | 138 | L 4-5 | 68-70 | 2 | 25,515 | Aaron Harang | Brad Hennessey | Kevin Correia | David Weathers | Mike Stanton | 670 | 703 | -33 |
| 2006-09-05 | vs SFN | 139 | W 3-0 | 69-70 | 2 | 20,751 | Bronson Arroyo | Matt Morris | Bronson Arroyo | Matt Morris | | 673 | 703 | -30 |
| 2006-09-06 | vs SFN | 140 | L 2-3 | 69-71 | 2 | 20,571 | Sun-Woo Kim | Jonathan Sanchez | Jonathan Sanchez | Sun-Woo Kim | Mike Stanton | 675 | 706 | -31 |
| 2006-09-08 | vs PIT | 141 | W 9-1 | 70-71 | 2 | 17,631 | Kyle Lohse | Ian Snell | Kyle Lohse | Ian Snell | | 684 | 707 | -23 |
| 2006-09-09 | vs PIT | 142 | L 4-7 | 70-72 | 3 | 25,038 | Aaron Harang | Paul Maholm | Matt Capps | Todd Coffey | Salomon Torres | 688 | 714 | -26 |
| 2006-09-10 | vs PIT | 143 | W 4-2 | 71-72 | 2 | 20,731 | Bronson Arroyo | Shane Youman | Bronson Arroyo | Shane Youman | Scott Schoeneweis | 692 | 716 | -24 |
| 2006-09-12 | vs SDN | 144 | W 5-4 | 72-72 | 2 | 15,820 | Eric Milton | Chris Young | Scott Schoeneweis | Doug Brocail | | 697 | 720 | -23 |
| 2006-09-13 | vs SDN | 145 | L 0-10 | 72-73 | 2 | 21,602 | Kyle Lohse | Jake Peavy | Jake Peavy | Kyle Lohse | | 697 | 730 | -33 |
| 2006-09-14 | vs SDN | 146 | L 2-4 | 72-74 | 2 | 16,957 | Aaron Harang | Clay Hensley | Clay Hensley | Aaron Harang | Trevor Hoffman | 699 | 734 | -35 |
| 2006-09-15 | @ CHN | 147 | W 4-0 | 73-74 | 2 | 37,188 | Bronson Arroyo | Juan Mateo | Bronson Arroyo | Carlos Marmol | | 703 | 734 | -31 |
| 2006-09-16 | @ CHN | 148 | L 0-4 | 73-75 | 2 | 40,526 | Chris Michalak | Rich Hill | Rich Hill | Chris Michalak | | 703 | 738 | -35 |
| 2006-09-17 | @ CHN | 149 | L 3-11 | 73-76 | 2 | 39,164 | Eric Milton | Carlos Zambrano | Carlos Zambrano | Eric Milton | | 706 | 749 | -43 |
| 2006-09-18 | @ HOU | 150 | L 3-5 | 73-77 | 2 | 28,711 | Kyle Lohse | Roy Oswalt | Roy Oswalt | Kyle Lohse | Dan Wheeler | 709 | 754 | -45 |
| 2006-09-19 | @ HOU | 151 | W 5-4 | 74-77 | 2 | 36,930 | Aaron Harang | Matt Albers | Aaron Harang | Matt Albers | David Weathers | 714 | 758 | -44 |
| 2006-09-20 | @ HOU | 152 | L 2-7 | 74-78 | 2 | 31,928 | Bronson Arroyo | Roger Clemens | Roger Clemens | Bronson Arroyo | | 716 | 765 | -49 |
| 2006-09-22 | vs CHN | 153 | W 4-2 | 75-78 | 2 | 21,332 | Chris Michalak | Rich Hill | Chris Michalak | Rich Hill | Todd Coffey | 720 | 767 | -47 |
| 2006-09-23 | vs CHN | 154 | L 4-11 | 75-79 | 3 | 28,264 | Kyle Lohse | Carlos Zambrano | Carlos Zambrano | Kyle Lohse | | 724 | 778 | -54 |
| 2006-09-24 | vs CHN | 155 | W 3-2 | 76-79 | 3 | 22,226 | Aaron Harang | Juan Mateo | Aaron Harang | Ryan Dempster | | 727 | 780 | -53 |
| 2006-09-25 | vs CHN | 156 | W 5-4 | 77-79 | 3 | 16,278 | Bronson Arroyo | Wade Miller | Scott Schoeneweis | Scott Eyre | David Weathers | 732 | 784 | -52 |
| 2006-09-26 | @ FLO | 157 | W 5-3 | 78-79 | 3 | 11,422 | Matt Belisle | Dontrelle Willis | Ryan Franklin | Dontrelle Willis | Scott Schoeneweis | 737 | 787 | -50 |
| 2006-09-27 | @ FLO | 158 | L 2-7 | 78-80 | 3 | 13,295 | Chris Michalak | Anibal Sanchez | Anibal Sanchez | Chris Michalak | | 739 | 794 | -55 |
| 2006-09-28 | @ FLO | 159 | W 5-1 | 79-80 | 3 | 14,106 | Kyle Lohse | Ricky Nolasco | Kyle Lohse | Ricky Nolasco | | 744 | 795 | -51 |
| 2006-09-29 | @ PIT | 160 | W 5-2 | 80-80 | 3 | 27,033 | Aaron Harang | Zach Duke | Aaron Harang | Zach Duke | | 749 | 797 | -48 |
| 2006-09-30 | @ PIT | 161 | L 0-3 | 80-81 | 3 | 35,514 | Bronson Arroyo | Marty McLeary | Marty McLeary | Bronson Arroyo | Salomon Torres | 749 | 800 | -51 |
| 2006-10-01 | @ PIT | 162 | L 0-1 | 80-82 | 3 | 25,004 | Matt Belisle | Shane Youman | Matt Capps | Todd Coffey | Salomon Torres | 749 | 801 | -52 |