| 2006-04-03 | @ CIN | 1 | W 16-7 | 1-0 | 1 | 42,591 | Carlos Zambrano | Aaron Harang | Will Ohman | Aaron Harang | | 16 | 7 | 9 |
| 2006-04-05 | @ CIN | 2 | L 6-8 | 1-1 | 4 | 27,287 | Glendon Rusch | Bronson Arroyo | Bronson Arroyo | Glendon Rusch | David Weathers | 22 | 15 | 7 |
| 2006-04-07 | vs SLN | 3 | W 5-1 | 2-1 | 5 | 40,869 | Greg Maddux | Jeff Suppan | Greg Maddux | Jeff Suppan | | 27 | 16 | 11 |
| 2006-04-08 | vs SLN | 4 | W 3-2 | 3-1 | 3 | 40,182 | Carlos Zambrano | Chris Carpenter | Bob Howry | Brad Thompson | Ryan Dempster | 30 | 18 | 12 |
| 2006-04-09 | vs SLN | 5 | W 8-4 | 4-1 | 2 | 39,839 | Sean Marshall | Sidney Ponson | Scott Williamson | Jason Isringhausen | | 38 | 22 | 16 |
| 2006-04-11 | vs CIN | 6 | L 2-9 | 4-2 | 4 | 36,708 | Glendon Rusch | Bronson Arroyo | Bronson Arroyo | Glendon Rusch | | 40 | 31 | 9 |
| 2006-04-12 | vs CIN | 7 | W 4-1 | 5-2 | 1 | 37,252 | Greg Maddux | Brandon Claussen | Greg Maddux | Brandon Claussen | Ryan Dempster | 44 | 32 | 12 |
| 2006-04-13 | vs CIN | 8 | L 3-8 | 5-3 | 4 | 40,881 | Carlos Zambrano | Eric Milton | Eric Milton | Carlos Zambrano | | 47 | 40 | 7 |
| 2006-04-14 | @ PIT | 9 | W 11-6 | 6-3 | 2 | 20,233 | Sean Marshall | Victor Santos | Sean Marshall | Victor Santos | | 58 | 46 | 12 |
| 2006-04-15 | @ PIT | 10 | L 1-2 | 6-4 | 4 | 34,264 | Jerome Williams | Zach Duke | Zach Duke | Jerome Williams | Mike Gonzalez | 59 | 48 | 11 |
| 2006-04-16 | @ PIT | 11 | W 7-3 | 7-4 | 2 | 15,020 | Glendon Rusch | Ian Snell | Glendon Rusch | Ian Snell | | 66 | 51 | 15 |
| 2006-04-17 | @ LAN | 12 | W 4-1 | 8-4 | 2 | 33,511 | Greg Maddux | Brett Tomko | Greg Maddux | Brett Tomko | Ryan Dempster | 70 | 52 | 18 |
| 2006-04-18 | @ LAN | 13 | L 1-2 | 8-5 | 2 | 37,342 | Carlos Zambrano | Derek Lowe | Takashi Saito | Will Ohman | | 71 | 54 | 17 |
| 2006-04-19 | @ LAN | 14 | W 5-4 | 9-5 | 2 | 41,288 | Sean Marshall | Brad Penny | Scott Williamson | Danys Baez | Ryan Dempster | 76 | 58 | 18 |
| 2006-04-21 | @ SLN | 15 | L 3-9 | 9-6 | 4 | 41,379 | Jerome Williams | Mark Mulder | Mark Mulder | Jerome Williams | | 79 | 67 | 12 |
| 2006-04-22 | @ SLN | 16 | L 1-4 | 9-7 | 4 | 41,424 | Glendon Rusch | Sidney Ponson | Sidney Ponson | Glendon Rusch | Jason Isringhausen | 80 | 71 | 9 |
| 2006-04-23 | @ SLN | 17 | W 7-3 | 10-7 | 4 | 41,373 | Greg Maddux | Jason Marquis | Greg Maddux | Jason Marquis | | 87 | 74 | 13 |
| 2006-04-24 | vs FLO | 18 | W 6-3 | 11-7 | 4 | 36,865 | Carlos Zambrano | Jason Vargas | David Aardsma | Josh Johnson | Ryan Dempster | 93 | 77 | 16 |
| 2006-04-25 | vs FLO | 19 | W 3-1 | 12-7 | 4 | 38,680 | Sean Marshall | Dontrelle Willis | Sean Marshall | Dontrelle Willis | Ryan Dempster | 96 | 78 | 18 |
| 2006-04-26 | vs FLO | 20 | L 5-7 | 12-8 | 4 | 39,611 | Angel Guzman | Scott Olsen | Ricky Nolasco | Scott Williamson | Joe Borowski | 101 | 85 | 16 |
| 2006-04-28 | vs MIL | 21 | W 6-2 | 13-8 | 4 | 39,522 | Greg Maddux | David Bush | Greg Maddux | David Bush | | 107 | 87 | 20 |
| 2006-04-29 | vs MIL | 22 | L 2-16 | 13-9 | 4 | 40,644 | Glendon Rusch | Doug Davis | Doug Davis | Glendon Rusch | | 109 | 103 | 6 |
| 2006-04-30 | vs MIL | 23 | L 0-9 | 13-10 | 4 | 39,229 | Carlos Zambrano | Chris Capuano | Chris Capuano | Carlos Zambrano | | 109 | 112 | -3 |
| 2006-05-01 | vs PIT | 24 | W 2-1 | 14-10 | 4 | 36,602 | Sean Marshall | Victor Santos | Bob Howry | John Grabow | Ryan Dempster | 111 | 113 | -2 |
| 2006-05-02 | vs PIT | 25 | L 0-8 | 14-11 | 4 | 39,110 | Angel Guzman | Zach Duke | Zach Duke | Angel Guzman | | 111 | 121 | -10 |
| 2006-05-03 | @ ARI | 26 | L 1-5 | 14-12 | 4 | 25,331 | Greg Maddux | Miguel Batista | Miguel Batista | Greg Maddux | Jose Valverde | 112 | 126 | -14 |
| 2006-05-04 | @ ARI | 27 | L 0-6 | 14-13 | 5 | 24,552 | Rich Hill | Juan Cruz | Juan Cruz | Rich Hill | | 112 | 132 | -20 |
| 2006-05-05 | @ SDN | 28 | L 0-1 | 14-14 | 5 | 37,123 | Carlos Zambrano | Chan Ho Park | Scott Cassidy | Scott Williamson | | 112 | 133 | -21 |
| 2006-05-06 | @ SDN | 29 | L 1-2 | 14-15 | 5 | 37,745 | Sean Marshall | Jake Peavy | Scott Cassidy | Bob Howry | | 113 | 135 | -22 |
| 2006-05-07 | @ SDN | 30 | L 3-6 | 14-16 | 5 | 39,847 | Angel Guzman | Woody Williams | Woody Williams | Angel Guzman | Brian Sweeney | 116 | 141 | -25 |
| 2006-05-08 | @ SDN | 31 | L 3-8 | 14-17 | 5 | 24,139 | Greg Maddux | Chris Young | Chris Young | Greg Maddux | | 119 | 149 | -30 |
| 2006-05-09 | @ SFN | 32 | L 1-6 | 14-18 | 5 | 39,357 | Rich Hill | Jason Schmidt | Jason Schmidt | Rich Hill | | 120 | 155 | -35 |
| 2006-05-10 | @ SFN | 33 | W 8-1 | 15-18 | 5 | 39,655 | Carlos Zambrano | Matt Cain | Carlos Zambrano | Matt Cain | | 128 | 156 | -28 |
| 2006-05-11 | @ SFN | 34 | L 3-9 | 15-19 | 5 | 38,132 | Sean Marshall | Jamey Wright | Jamey Wright | Sean Marshall | | 131 | 165 | -34 |
| 2006-05-12 | vs SDN | 35 | L 5-10 | 15-20 | 5 | 39,245 | Angel Guzman | Woody Williams | Brian Sweeney | Glendon Rusch | | 136 | 175 | -39 |
| 2006-05-13 | vs SDN | 36 | L 3-4 | 15-21 | 5 | 40,095 | Greg Maddux | Chris Young | Cla Meredith | Ryan Dempster | Trevor Hoffman | 139 | 179 | -40 |
| 2006-05-14 | vs SDN | 37 | L 0-9 | 15-22 | 5 | 39,570 | Rich Hill | Clay Hensley | Clay Hensley | Rich Hill | | 139 | 188 | -49 |
| 2006-05-16 | vs WAS | 38 | W 4-0 | 16-22 | 5 | 39,298 | Carlos Zambrano | Livan Hernandez | Carlos Zambrano | Livan Hernandez | | 143 | 188 | -45 |
| 2006-05-17 | vs WAS | 39 | W 5-0 | 17-22 | 5 | 39,757 | Sean Marshall | Zach Day | Sean Marshall | Zach Day | | 148 | 188 | -40 |
| 2006-05-18 | vs WAS | 40 | L 3-5 | 17-23 | 5 | 40,517 | Kerry Wood | Ramon Ortiz | Ramon Ortiz | Kerry Wood | Chad Cordero | 151 | 193 | -42 |
| 2006-05-19 | @ CHA | 41 | L 1-6 | 17-24 | 5 | 39,301 | Greg Maddux | Mark Buehrle | Mark Buehrle | Greg Maddux | | 152 | 199 | -47 |
| 2006-05-20 | @ CHA | 42 | L 0-7 | 17-25 | 5 | 39,387 | Rich Hill | Freddy Garcia | Freddy Garcia | Rich Hill | | 152 | 206 | -54 |
| 2006-05-21 | @ CHA | 43 | W 7-4 | 18-25 | 5 | 38,645 | Carlos Zambrano | Jose Contreras | Carlos Zambrano | Neal Cotts | Ryan Dempster | 159 | 210 | -51 |
| 2006-05-22 | @ FLO | 44 | L 1-9 | 18-26 | 5 | 9,462 | Sean Marshall | Ricky Nolasco | Ricky Nolasco | Sean Marshall | | 160 | 219 | -59 |
| 2006-05-23 | @ FLO | 45 | L 4-5 | 18-27 | 5 | 10,979 | Kerry Wood | Scott Olsen | Logan Kensing | Ryan Dempster | | 164 | 224 | -60 |
| 2006-05-24 | @ FLO | 46 | L 3-9 | 18-28 | 5 | 7,720 | Greg Maddux | Brian Moehler | Brian Moehler | Greg Maddux | | 167 | 233 | -66 |
| 2006-05-26 | vs ATL | 47 | L 5-6 | 18-29 | 5 | 40,865 | Carlos Zambrano | Tim Hudson | Mike Remlinger | Ryan Dempster | Ken Ray | 172 | 239 | -67 |
| 2006-05-27 | vs ATL | 48 | L 1-2 | 18-30 | 5 | 41,526 | Sean Marshall | Horacio Ramirez | Horacio Ramirez | Sean Marshall | Mike Remlinger | 173 | 241 | -68 |
| 2006-05-28 | vs ATL | 49 | L 12-13 | 18-31 | 5 | 41,698 | Jae Kuk Ryu | John Smoltz | Oscar Villarreal | Scott Eyre | Ken Ray | 185 | 254 | -69 |
| 2006-05-29 | vs CIN | 50 | W 7-3 | 19-31 | 5 | 40,072 | Kerry Wood | Elizardo Ramirez | Kerry Wood | Elizardo Ramirez | Ryan Dempster | 192 | 257 | -65 |
| 2006-05-30 | vs CIN | 51 | W 8-3 | 20-31 | 5 | 39,000 | Greg Maddux | Brandon Claussen | Greg Maddux | Brandon Claussen | | 200 | 260 | -60 |
| 2006-05-31 | vs CIN | 52 | L 2-3 | 20-32 | 5 | 39,810 | Carlos Zambrano | Eric Milton | Eric Milton | Carlos Zambrano | Todd Coffey | 202 | 263 | -61 |
| 2006-06-02 | @ SLN | 53 | W 5-4 | 21-32 | 5 | 45,799 | Sean Marshall | Sidney Ponson | Ryan Dempster | Josh Hancock | | 207 | 267 | -60 |
| 2006-06-03 | @ SLN | 54 | W 8-5 | 22-32 | 5 | 45,820 | Glendon Rusch | Mark Mulder | Glendon Rusch | Mark Mulder | Bob Howry | 215 | 272 | -57 |
| 2006-06-04 | @ SLN | 55 | L 6-9 | 22-33 | 5 | 45,753 | Greg Maddux | Jason Marquis | Jason Marquis | Greg Maddux | Jason Isringhausen | 221 | 281 | -60 |
| 2006-06-05 | @ HOU | 56 | W 8-0 | 23-33 | 5 | 32,814 | Carlos Zambrano | Taylor Buchholz | Carlos Zambrano | Taylor Buchholz | | 229 | 281 | -52 |
| 2006-06-06 | @ HOU | 57 | L 1-4 | 23-34 | 5 | 35,903 | Kerry Wood | Wandy Rodriguez | Wandy Rodriguez | Kerry Wood | | 230 | 285 | -55 |
| 2006-06-07 | @ HOU | 58 | L 0-1 | 23-35 | 5 | 42,492 | Sean Marshall | Chris Sampson | Chris Sampson | Sean Marshall | Brad Lidge | 230 | 286 | -56 |
| 2006-06-08 | @ CIN | 59 | L 1-7 | 23-36 | 5 | 26,059 | Glendon Rusch | Bronson Arroyo | Bronson Arroyo | Glendon Rusch | | 231 | 293 | -62 |
| 2006-06-09 | @ CIN | 60 | W 6-5 | 24-36 | 5 | 41,064 | Greg Maddux | Elizardo Ramirez | Greg Maddux | Elizardo Ramirez | Ryan Dempster | 237 | 298 | -61 |
| 2006-06-10 | @ CIN | 61 | W 4-2 | 25-36 | 5 | 34,141 | Carlos Zambrano | Brandon Claussen | Carlos Zambrano | Brandon Claussen | Ryan Dempster | 241 | 300 | -59 |
| 2006-06-11 | @ CIN | 62 | W 9-3 | 26-36 | 5 | 27,250 | Carlos Marmol | Eric Milton | Carlos Marmol | Eric Milton | | 250 | 303 | -53 |
| 2006-06-13 | vs HOU | 63 | L 2-9 | 26-37 | 5 | 40,563 | Sean Marshall | Andy Pettitte | Andy Pettitte | Sean Marshall | | 252 | 312 | -60 |
| 2006-06-14 | vs HOU | 64 | L 4-5 | 26-38 | 5 | 39,946 | Greg Maddux | Roy Oswalt | Roy Oswalt | Greg Maddux | Brad Lidge | 256 | 317 | -61 |
| 2006-06-15 | vs HOU | 65 | L 2-3 | 26-39 | 5 | 40,236 | Carlos Zambrano | Fernando Nieve | Dave Borkowski | Bob Howry | Brad Lidge | 258 | 320 | -62 |
| 2006-06-16 | vs DET | 66 | L 3-5 | 26-40 | 5 | 40,683 | Glendon Rusch | Nate Robertson | Nate Robertson | Glendon Rusch | Todd Jones | 261 | 325 | -64 |
| 2006-06-17 | vs DET | 67 | L 3-9 | 26-41 | 5 | 41,459 | Carlos Marmol | Justin Verlander | Justin Verlander | Carlos Marmol | | 264 | 334 | -70 |
| 2006-06-18 | vs DET | 68 | L 3-12 | 26-42 | 5 | 39,938 | Mark Prior | Kenny Rogers | Kenny Rogers | Mark Prior | | 267 | 346 | -79 |
| 2006-06-19 | @ CLE | 69 | W 12-8 | 27-42 | 5 | 26,769 | Sean Marshall | Jason Johnson | Sean Marshall | Jason Johnson | | 279 | 354 | -75 |
| 2006-06-20 | @ CLE | 70 | L 2-4 | 27-43 | 5 | 25,049 | Greg Maddux | Cliff Lee | Cliff Lee | Greg Maddux | Bob Wickman | 281 | 358 | -77 |
| 2006-06-21 | @ CLE | 71 | W 9-2 | 28-43 | 5 | 27,182 | Carlos Zambrano | CC Sabathia | Carlos Zambrano | CC Sabathia | | 290 | 360 | -70 |
| 2006-06-23 | @ MIN | 72 | L 2-7 | 28-44 | 5 | 34,361 | Carlos Marmol | Johan Santana | Johan Santana | Carlos Marmol | | 292 | 367 | -75 |
| 2006-06-24 | @ MIN | 73 | L 0-3 | 28-45 | 5 | 42,304 | Mark Prior | Boof Bonser | Boof Bonser | Mark Prior | Joe Nathan | 292 | 370 | -78 |
| 2006-06-25 | @ MIN | 74 | L 1-8 | 28-46 | 5 | 35,128 | Sean Marshall | Brad Radke | Brad Radke | Sean Marshall | | 293 | 378 | -85 |
| 2006-06-26 | vs MIL | 75 | L 0-6 | 28-47 | 5 | 39,698 | Greg Maddux | Chris Capuano | Chris Capuano | Greg Maddux | | 293 | 384 | -91 |
| 2006-06-27 | vs MIL | 76 | L 5-8 | 28-48 | 5 | 39,399 | Carlos Zambrano | Zach Jackson | Brian Shouse | Ryan Dempster | Derrick Turnbow | 298 | 392 | -94 |
| 2006-06-28 | vs MIL | 77 | W 6-3 | 29-48 | 5 | 39,321 | Carlos Marmol | David Bush | Bob Howry | Danny Kolb | Ryan Dempster | 304 | 395 | -91 |
| 2006-06-29 | vs MIL | 78 | L 4-5 | 29-49 | 5 | 39,144 | Mark Prior | Geremi Gonzalez | Geremi Gonzalez | Mark Prior | Derrick Turnbow | 308 | 400 | -92 |
| 2006-06-30 | vs CHA | 79 | L 2-6 | 29-50 | 5 | 40,720 | Sean Marshall | Jon Garland | Jon Garland | Sean Marshall | | 310 | 406 | -96 |
| 2006-07-01 | vs CHA | 80 | L 6-8 | 29-51 | 5 | 41,027 | Greg Maddux | Javier Vazquez | Neal Cotts | Ryan Dempster | Bobby Jenks | 316 | 414 | -98 |
| 2006-07-02 | vs CHA | 81 | W 15-11 | 30-51 | 5 | 40,919 | Carlos Zambrano | Mark Buehrle | Carlos Zambrano | Mark Buehrle | Bob Howry | 331 | 425 | -94 |
| 2006-07-03 | @ HOU | 82 | L 2-7 | 30-52 | 5 | 41,655 | Carlos Marmol | Roger Clemens | Roger Clemens | Carlos Marmol | | 333 | 432 | -99 |
| 2006-07-04 | @ HOU | 83 | L 2-7 | 30-53 | 5 | 41,502 | Mark Prior | Andy Pettitte | Andy Pettitte | Mark Prior | | 335 | 439 | -104 |
| 2006-07-05 | @ HOU | 84 | W 1-0 | 31-53 | 5 | 31,952 | Sean Marshall | Roy Oswalt | Sean Marshall | Roy Oswalt | Ryan Dempster | 336 | 439 | -103 |
| 2006-07-06 | @ MIL | 85 | L 0-2 | 31-54 | 5 | 37,326 | Greg Maddux | Chris Capuano | Chris Capuano | Greg Maddux | | 336 | 441 | -105 |
| 2006-07-07 | @ MIL | 86 | W 7-2 | 32-54 | 5 | 41,172 | Carlos Zambrano | Zach Jackson | Carlos Zambrano | Zach Jackson | | 343 | 443 | -100 |
| 2006-07-08 | @ MIL | 87 | W 3-1 | 33-54 | 5 | 42,268 | Carlos Marmol | David Bush | Carlos Marmol | David Bush | Ryan Dempster | 346 | 444 | -98 |
| 2006-07-09 | @ MIL | 88 | W 11-4 | 34-54 | 5 | 41,528 | Glendon Rusch | Doug Davis | Glendon Rusch | Doug Davis | | 357 | 448 | -91 |
| 2006-07-14 | vs NYN | 89 | L 3-6 | 34-55 | 5 | 40,782 | Greg Maddux | Steve Trachsel | Steve Trachsel | Greg Maddux | | 360 | 454 | -94 |
| 2006-07-15 | vs NYN | 90 | W 9-2 | 35-55 | 5 | 41,368 | Carlos Zambrano | Tom Glavine | Carlos Zambrano | Tom Glavine | | 369 | 456 | -87 |
| 2006-07-16 | vs NYN | 91 | L 7-13 | 35-56 | 5 | 40,157 | Sean Marshall | Orlando Hernandez | Pedro Feliciano | Sean Marshall | | 376 | 469 | -93 |
| 2006-07-18 | vs HOU | 92 | W 4-2 | 36-56 | 5 | 39,883 | Carlos Marmol | Roy Oswalt | Carlos Marmol | Roy Oswalt | Ryan Dempster | 380 | 471 | -91 |
| 2006-07-19 | vs HOU | 93 | L 2-4 | 36-57 | 5 | 40,344 | Greg Maddux | Roger Clemens | Roger Clemens | Greg Maddux | Brad Lidge | 382 | 475 | -93 |
| 2006-07-20 | vs HOU | 94 | W 4-1 | 37-57 | 5 | 40,208 | Carlos Zambrano | Andy Pettitte | Carlos Zambrano | Andy Pettitte | Ryan Dempster | 386 | 476 | -90 |
| 2006-07-21 | @ WAS | 95 | L 6-7 | 37-58 | 5 | 35,442 | Mark Prior | Pedro Astacio | Jon Rauch | Bob Howry | Chad Cordero | 392 | 483 | -91 |
| 2006-07-22 | @ WAS | 96 | L 3-7 | 37-59 | 5 | 38,021 | Sean Marshall | Livan Hernandez | Livan Hernandez | Scott Williamson | | 395 | 490 | -95 |
| 2006-07-23 | @ WAS | 97 | L 1-7 | 37-60 | 5 | 30,851 | Carlos Marmol | Tony Armas | Tony Armas | Carlos Marmol | | 396 | 497 | -101 |
| 2006-07-24 | @ NYN | 98 | W 8-7 | 38-60 | 5 | 45,631 | Greg Maddux | Steve Trachsel | Greg Maddux | Steve Trachsel | Ryan Dempster | 404 | 504 | -100 |
| 2006-07-25 | @ NYN | 99 | W 8-6 | 39-60 | 5 | 47,686 | Carlos Zambrano | Tom Glavine | Carlos Zambrano | Tom Glavine | Bob Howry | 412 | 510 | -98 |
| 2006-07-26 | @ NYN | 100 | L 0-1 | 39-61 | 5 | 40,299 | Mark Prior | John Maine | Aaron Heilman | Glendon Rusch | | 412 | 511 | -99 |
| 2006-07-27 | vs SLN | 101 | W 5-4 | 40-61 | 5 | 40,346 | Rich Hill | Jeff Weaver | Roberto Novoa | Tyler Johnson | Ryan Dempster | 417 | 515 | -98 |
| 2006-07-28 | vs SLN | 102 | W 6-5 | 41-61 | 5 | 40,420 | Carlos Marmol | Jason Marquis | Carlos Marmol | Jason Marquis | Ryan Dempster | 423 | 520 | -97 |
| 2006-07-29 | vs SLN | 103 | W 4-2 | 42-61 | 5 | 41,302 | Greg Maddux | Anthony Reyes | Greg Maddux | Anthony Reyes | Ryan Dempster | 427 | 522 | -95 |
| 2006-07-30 | vs SLN | 104 | W 6-3 | 43-61 | 5 | 40,033 | Carlos Zambrano | Chris Carpenter | Carlos Zambrano | Chris Carpenter | | 433 | 525 | -92 |
| 2006-07-31 | vs ARI | 105 | L 4-15 | 43-62 | 5 | 39,226 | Mark Prior | Brandon Webb | Brandon Webb | Mark Prior | | 437 | 540 | -103 |
| 2006-08-01 | vs ARI | 106 | W 9-3 | 44-62 | 5 | 38,970 | Rich Hill | Claudio Vargas | Rich Hill | Claudio Vargas | | 446 | 543 | -97 |
| 2006-08-03 | vs ARI | 107 | L 2-10 | 45-63 | 5 | 0 | Carlos Marmol | Juan Cruz | Juan Cruz | Carlos Marmol | | 448 | 553 | -105 |
| 2006-08-03 | vs ARI | 108 | W 7-3 | 45-63 | 5 | 40,715 | Juan Mateo | Enrique Gonzalez | Juan Mateo | Enrique Gonzalez | | 455 | 556 | -101 |
| 2006-08-04 | vs PIT | 109 | L 0-6 | 45-64 | 5 | 39,973 | Carlos Zambrano | Tom Gorzelanny | Tom Gorzelanny | Carlos Zambrano | | 455 | 562 | -107 |
| 2006-08-05 | vs PIT | 110 | W 7-5 | 46-64 | 5 | 41,007 | Mark Prior | Zach Duke | Mark Prior | Zach Duke | Ryan Dempster | 462 | 567 | -105 |
| 2006-08-06 | vs PIT | 111 | W 6-1 | 47-64 | 5 | 40,320 | Rich Hill | Ian Snell | Rich Hill | Ian Snell | | 468 | 568 | -100 |
| 2006-08-08 | @ MIL | 112 | W 6-3 | 48-64 | 5 | 36,200 | Carlos Marmol | Tomo Ohka | Carlos Marmol | Tomo Ohka | Ryan Dempster | 474 | 571 | -97 |
| 2006-08-09 | @ MIL | 113 | L 3-6 | 48-65 | 5 | 36,012 | Carlos Zambrano | David Bush | David Bush | Carlos Zambrano | Francisco Cordero | 477 | 577 | -100 |
| 2006-08-10 | @ MIL | 114 | L 6-8 | 48-66 | 5 | 41,686 | Mark Prior | Doug Davis | Doug Davis | Mark Prior | Francisco Cordero | 483 | 585 | -102 |
| 2006-08-11 | @ COL | 115 | L 2-10 | 48-67 | 5 | 35,744 | Rich Hill | Aaron Cook | Aaron Cook | Rich Hill | | 485 | 595 | -110 |
| 2006-08-12 | @ COL | 116 | L 4-8 | 48-68 | 5 | 43,485 | Angel Guzman | Josh Fogg | Josh Fogg | Angel Guzman | | 489 | 603 | -114 |
| 2006-08-13 | @ COL | 117 | W 8-7 | 49-68 | 5 | 35,408 | Carlos Marmol | Byung-Hyun Kim | Roberto Novoa | Manuel Corpas | Ryan Dempster | 497 | 610 | -113 |
| 2006-08-14 | @ HOU | 118 | W 3-0 | 50-68 | 5 | 37,260 | Carlos Zambrano | Roy Oswalt | Carlos Zambrano | Roy Oswalt | Ryan Dempster | 500 | 610 | -110 |
| 2006-08-15 | @ HOU | 119 | W 8-6 | 51-68 | 5 | 41,531 | Juan Mateo | Roger Clemens | Rich Hill | Dave Borkowski | | 508 | 616 | -108 |
| 2006-08-16 | @ HOU | 120 | W 1-0 | 52-68 | 5 | 38,989 | Ryan O'Malley | Andy Pettitte | Ryan O'Malley | Andy Pettitte | Bob Howry | 509 | 616 | -107 |
| 2006-08-18 | vs SLN | 121 | L 3-11 | 52-69 | 5 | 40,346 | Carlos Marmol | Jason Marquis | Jason Marquis | Carlos Marmol | | 512 | 627 | -115 |
| 2006-08-19 | vs SLN | 122 | W 5-4 | 53-69 | 5 | 40,864 | Carlos Zambrano | Jeff Suppan | Michael Wuertz | Jason Isringhausen | | 517 | 631 | -114 |
| 2006-08-20 | vs SLN | 123 | L 3-5 | 53-70 | 5 | 40,485 | Juan Mateo | Chris Carpenter | Chris Carpenter | Juan Mateo | Jason Isringhausen | 520 | 636 | -116 |
| 2006-08-21 | vs PHI | 124 | L 5-6 | 53-71 | 5 | 38,950 | Rich Hill | Jon Lieber | Jon Lieber | Rich Hill | Arthur Rhodes | 525 | 642 | -117 |
| 2006-08-22 | vs PHI | 125 | L 3-6 | 53-72 | 5 | 38,770 | Ryan O'Malley | Jamie Moyer | Jamie Moyer | Ryan O'Malley | Ryan Madson | 528 | 648 | -120 |
| 2006-08-23 | vs PHI | 126 | L 1-2 | 53-73 | 5 | 39,470 | Angel Guzman | Brett Myers | Brett Myers | Bob Howry | Geoff Geary | 529 | 650 | -121 |
| 2006-08-24 | vs PHI | 127 | W 11-2 | 54-73 | 5 | 39,464 | Carlos Zambrano | Cole Hamels | Carlos Zambrano | Cole Hamels | | 540 | 652 | -112 |
| 2006-08-25 | @ SLN | 128 | L 0-2 | 54-74 | 5 | 46,004 | Juan Mateo | Jeff Suppan | Jeff Suppan | Juan Mateo | Jason Isringhausen | 540 | 654 | -114 |
| 2006-08-26 | @ SLN | 129 | L 1-2 | 54-75 | 5 | 46,036 | Rich Hill | Chris Carpenter | Randy Flores | Roberto Novoa | | 541 | 656 | -115 |
| 2006-08-27 | @ SLN | 130 | L 6-10 | 54-76 | 5 | 44,937 | Les Walrond | Jeff Weaver | Braden Looper | Bob Howry | | 547 | 666 | -119 |
| 2006-08-28 | @ PIT | 131 | L 6-11 | 54-77 | 5 | 12,666 | Angel Guzman | Ian Snell | Ian Snell | Angel Guzman | | 553 | 677 | -124 |
| 2006-08-29 | @ PIT | 132 | L 6-7 | 54-78 | 5 | 14,618 | Carlos Zambrano | Paul Maholm | Matt Capps | Ryan Dempster | | 559 | 684 | -125 |
| 2006-08-30 | @ PIT | 133 | L 9-10 | 54-79 | 5 | 12,730 | Juan Mateo | Victor Santos | Marty McLeary | Ryan Dempster | | 568 | 694 | -126 |
| 2006-09-01 | vs SFN | 134 | W 6-2 | 55-79 | 5 | 38,582 | Rich Hill | Noah Lowry | Rich Hill | Noah Lowry | | 574 | 696 | -122 |
| 2006-09-02 | vs SFN | 135 | L 2-4 | 55-80 | 5 | 40,135 | Sean Marshall | Matt Cain | Matt Cain | Sean Marshall | Mike Stanton | 576 | 700 | -124 |
| 2006-09-03 | vs SFN | 136 | L 4-7 | 55-81 | 5 | 40,702 | Angel Guzman | Jason Schmidt | Jason Schmidt | Michael Wuertz | Mike Stanton | 580 | 707 | -127 |
| 2006-09-04 | vs PIT | 137 | L 4-5 | 55-82 | 5 | 37,994 | Carlos Zambrano | Paul Maholm | Paul Maholm | Carlos Zambrano | Salomon Torres | 584 | 712 | -128 |
| 2006-09-05 | vs PIT | 138 | L 5-6 | 55-83 | 6 | 31,494 | Juan Mateo | Victor Santos | John Grabow | Ryan Dempster | Salomon Torres | 589 | 718 | -129 |
| 2006-09-06 | vs PIT | 139 | W 7-2 | 56-83 | 5 | 32,557 | Rich Hill | Zach Duke | Michael Wuertz | John Grabow | | 596 | 720 | -124 |
| 2006-09-07 | vs PIT | 140 | L 5-7 | 56-84 | 6 | 27,105 | Sean Marshall | Shawn Chacon | Jonah Bayliss | Scott Eyre | Salomon Torres | 601 | 727 | -126 |
| 2006-09-08 | @ ATL | 141 | L 4-8 | 56-85 | 6 | 30,977 | Angel Guzman | Tim Hudson | Tim Hudson | Angel Guzman | | 605 | 735 | -130 |
| 2006-09-09 | @ ATL | 142 | L 3-7 | 56-86 | 6 | 40,584 | Wade Miller | Chuck James | Chuck James | Wade Miller | | 608 | 742 | -134 |
| 2006-09-10 | @ ATL | 143 | L 1-2 | 56-87 | 6 | 28,212 | Juan Mateo | Lance Cormier | Lance Cormier | Juan Mateo | Bob Wickman | 609 | 744 | -135 |
| 2006-09-11 | @ ATL | 144 | W 8-3 | 57-87 | 6 | 19,444 | Rich Hill | John Smoltz | Rich Hill | John Smoltz | | 617 | 747 | -130 |
| 2006-09-12 | vs LAN | 145 | W 9-8 | 58-87 | 6 | 35,618 | Sean Marshall | Derek Lowe | David Aardsma | Tim Hamulack | | 626 | 755 | -129 |
| 2006-09-13 | vs LAN | 146 | L 0-6 | 58-88 | 6 | 35,868 | Angel Guzman | Brad Penny | Brad Penny | Angel Guzman | | 626 | 761 | -135 |
| 2006-09-14 | vs LAN | 147 | W 6-5 | 59-88 | 6 | 31,361 | Wade Miller | Hong-Chih Kuo | Scott Eyre | Brett Tomko | Bob Howry | 632 | 766 | -134 |
| 2006-09-15 | vs CIN | 148 | L 0-4 | 59-89 | 6 | 37,188 | Juan Mateo | Bronson Arroyo | Bronson Arroyo | Carlos Marmol | | 632 | 770 | -138 |
| 2006-09-16 | vs CIN | 149 | W 4-0 | 60-89 | 6 | 40,526 | Rich Hill | Chris Michalak | Rich Hill | Chris Michalak | | 636 | 770 | -134 |
| 2006-09-17 | vs CIN | 150 | W 11-3 | 61-89 | 6 | 39,164 | Carlos Zambrano | Eric Milton | Carlos Zambrano | Eric Milton | | 647 | 773 | -126 |
| 2006-09-18 | @ PHI | 151 | W 11-6 | 62-89 | 6 | 31,101 | Sean Marshall | Jon Lieber | Michael Wuertz | Jon Lieber | | 658 | 779 | -121 |
| 2006-09-19 | @ PHI | 152 | L 1-4 | 62-90 | 6 | 31,892 | Wade Miller | Jamie Moyer | Jamie Moyer | Wade Miller | Tom Gordon | 659 | 783 | -124 |
| 2006-09-20 | @ PHI | 153 | L 2-6 | 62-91 | 6 | 35,269 | Les Walrond | Brett Myers | Brett Myers | Les Walrond | | 661 | 789 | -128 |
| 2006-09-22 | @ CIN | 154 | L 2-4 | 62-92 | 6 | 21,332 | Rich Hill | Chris Michalak | Chris Michalak | Rich Hill | Todd Coffey | 663 | 793 | -130 |
| 2006-09-23 | @ CIN | 155 | W 11-4 | 63-92 | 6 | 28,264 | Carlos Zambrano | Kyle Lohse | Carlos Zambrano | Kyle Lohse | | 674 | 797 | -123 |
| 2006-09-24 | @ CIN | 156 | L 2-3 | 63-93 | 6 | 22,226 | Juan Mateo | Aaron Harang | Aaron Harang | Ryan Dempster | | 676 | 800 | -124 |
| 2006-09-25 | @ CIN | 157 | L 4-5 | 63-94 | 6 | 16,278 | Wade Miller | Bronson Arroyo | Scott Schoeneweis | Scott Eyre | David Weathers | 680 | 805 | -125 |
| 2006-09-26 | vs MIL | 158 | W 14-6 | 64-94 | 6 | 31,932 | Sean Marshall | Carlos Villanueva | Sean Marshall | Carlos Villanueva | | 694 | 811 | -117 |
| 2006-09-27 | vs MIL | 159 | W 3-2 | 65-94 | 6 | 36,273 | Rich Hill | David Bush | Bob Howry | Francisco Cordero | | 697 | 813 | -116 |
| 2006-09-29 | vs COL | 160 | L 2-5 | 65-95 | 5 | 33,721 | Carlos Zambrano | Josh Fogg | Josh Fogg | Carlos Zambrano | Brian Fuentes | 699 | 818 | -119 |
| 2006-09-30 | vs COL | 161 | L 9-11 | 65-96 | 6 | 39,483 | Juan Mateo | Jeff Francis | Ramon Ramirez | Jae Kuk Ryu | | 708 | 829 | -121 |
| 2006-10-01 | vs COL | 162 | W 8-5 | 66-96 | 6 | 39,609 | Wade Miller | Ubaldo Jimenez | David Aardsma | Jeremy Affeldt | | 716 | 834 | -118 |