| 2006-04-03 | @ MIL | 1 | L 2-5 | 0-1 | 6 | 45,023 | Oliver Perez | Doug Davis | Justin Lehr | Salomon Torres | Derrick Turnbow | 2 | 5 | -3 |
| 2006-04-04 | @ MIL | 2 | L 5-7 | 0-2 | 6 | 15,515 | Victor Santos | Chris Capuano | Chris Capuano | Victor Santos | Derrick Turnbow | 7 | 12 | -5 |
| 2006-04-05 | @ MIL | 3 | L 2-3 | 0-3 | 6 | 15,430 | Zach Duke | Tomo Ohka | Matt Wise | Damaso Marte | Derrick Turnbow | 9 | 15 | -6 |
| 2006-04-06 | @ CIN | 4 | L 5-6 | 0-4 | 6 | 13,887 | Ian Snell | Brandon Claussen | Rick White | Mike Gonzalez | David Weathers | 14 | 21 | -7 |
| 2006-04-07 | @ CIN | 5 | L 6-7 | 0-5 | 6 | 16,573 | Paul Maholm | Eric Milton | Eric Milton | Paul Maholm | Kent Mercker | 20 | 28 | -8 |
| 2006-04-08 | @ CIN | 6 | L 9-11 | 0-6 | 6 | 20,244 | Oliver Perez | Aaron Harang | Aaron Harang | Oliver Perez | Rick White | 29 | 39 | -10 |
| 2006-04-09 | @ CIN | 7 | W 5-3 | 1-6 | 6 | 22,090 | Victor Santos | David Williams | Victor Santos | David Williams | Roberto Hernandez | 34 | 42 | -8 |
| 2006-04-10 | vs LAN | 8 | L 3-8 | 1-7 | 6 | 39,129 | Zach Duke | Odalis Perez | Odalis Perez | Zach Duke | | 37 | 50 | -13 |
| 2006-04-11 | vs LAN | 9 | W 7-6 | 2-7 | 6 | 17,240 | Ian Snell | Jae Weong Seo | Salomon Torres | Lance Carter | Mike Gonzalez | 44 | 56 | -12 |
| 2006-04-12 | vs LAN | 10 | W 9-5 | 3-7 | 6 | 13,237 | Paul Maholm | Brett Tomko | Salomon Torres | Hong-Chih Kuo | | 53 | 61 | -8 |
| 2006-04-13 | vs LAN | 11 | L 5-13 | 3-8 | 6 | 18,134 | Oliver Perez | Derek Lowe | Derek Lowe | Oliver Perez | | 58 | 74 | -16 |
| 2006-04-14 | vs CHN | 12 | L 6-11 | 3-9 | 6 | 20,233 | Victor Santos | Sean Marshall | Sean Marshall | Victor Santos | | 64 | 85 | -21 |
| 2006-04-15 | vs CHN | 13 | W 2-1 | 4-9 | 6 | 34,264 | Zach Duke | Jerome Williams | Zach Duke | Jerome Williams | Mike Gonzalez | 66 | 86 | -20 |
| 2006-04-16 | vs CHN | 14 | L 3-7 | 4-10 | 6 | 15,020 | Ian Snell | Glendon Rusch | Glendon Rusch | Ian Snell | | 69 | 93 | -24 |
| 2006-04-17 | vs SLN | 15 | L 1-2 | 4-11 | 6 | 15,278 | Paul Maholm | Jason Marquis | Jason Marquis | Paul Maholm | Jason Isringhausen | 70 | 95 | -25 |
| 2006-04-18 | vs SLN | 16 | W 12-4 | 5-11 | 6 | 16,682 | Oliver Perez | Jeff Suppan | Oliver Perez | Jeff Suppan | | 82 | 99 | -17 |
| 2006-04-19 | vs SLN | 17 | L 0-4 | 5-12 | 6 | 15,085 | Victor Santos | Chris Carpenter | Chris Carpenter | Victor Santos | | 82 | 103 | -21 |
| 2006-04-21 | @ HOU | 18 | L 2-3 | 5-13 | 6 | 31,333 | Zach Duke | Wandy Rodriguez | Wandy Rodriguez | Zach Duke | Brad Lidge | 84 | 106 | -22 |
| 2006-04-22 | @ HOU | 19 | L 0-3 | 5-14 | 6 | 38,575 | Ian Snell | Taylor Buchholz | Taylor Buchholz | Ian Snell | Brad Lidge | 84 | 109 | -25 |
| 2006-04-23 | @ HOU | 20 | L 2-7 | 5-15 | 6 | 39,074 | Paul Maholm | Roy Oswalt | Roy Oswalt | Paul Maholm | | 86 | 116 | -30 |
| 2006-04-24 | @ SLN | 21 | L 2-7 | 5-16 | 6 | 38,953 | Oliver Perez | Chris Carpenter | Chris Carpenter | Oliver Perez | | 88 | 123 | -35 |
| 2006-04-25 | @ SLN | 22 | L 3-6 | 5-17 | 6 | 38,809 | Victor Santos | Jeff Suppan | Jeff Suppan | Victor Santos | Jason Isringhausen | 91 | 129 | -38 |
| 2006-04-26 | @ SLN | 23 | L 3-4 | 5-18 | 6 | 38,728 | Zach Duke | Mark Mulder | Jason Isringhausen | Roberto Hernandez | | 94 | 133 | -39 |
| 2006-04-28 | vs PHI | 24 | W 3-1 | 6-18 | 6 | 30,568 | Ian Snell | Brett Myers | Ian Snell | Brett Myers | Mike Gonzalez | 97 | 134 | -37 |
| 2006-04-29 | vs PHI | 25 | W 3-2 | 7-18 | 6 | 33,944 | Paul Maholm | Cory Lidle | Paul Maholm | Cory Lidle | Roberto Hernandez | 100 | 136 | -36 |
| 2006-04-30 | vs PHI | 26 | L 1-5 | 7-19 | 6 | 22,320 | Oliver Perez | Gavin Floyd | Gavin Floyd | Oliver Perez | | 101 | 141 | -40 |
| 2006-05-01 | @ CHN | 27 | L 1-2 | 7-20 | 6 | 36,602 | Victor Santos | Sean Marshall | Bob Howry | John Grabow | Ryan Dempster | 102 | 143 | -41 |
| 2006-05-02 | @ CHN | 28 | W 8-0 | 8-20 | 6 | 39,110 | Zach Duke | Angel Guzman | Zach Duke | Angel Guzman | | 110 | 143 | -33 |
| 2006-05-03 | @ NYN | 29 | L 3-4 | 8-21 | 6 | 33,668 | Ian Snell | Pedro Martinez | Chad Bradford | Mike Gonzalez | | 113 | 147 | -34 |
| 2006-05-04 | @ NYN | 30 | L 0-6 | 8-22 | 6 | 30,756 | Paul Maholm | Tom Glavine | Tom Glavine | Paul Maholm | | 113 | 153 | -40 |
| 2006-05-05 | @ WAS | 31 | L 0-6 | 8-23 | 6 | 21,059 | Oliver Perez | Zach Day | Zach Day | Oliver Perez | | 113 | 159 | -46 |
| 2006-05-06 | @ WAS | 32 | W 5-4 | 9-23 | 6 | 29,953 | Victor Santos | Ramon Ortiz | Mike Gonzalez | Felix Rodriguez | | 118 | 163 | -45 |
| 2006-05-07 | @ WAS | 33 | L 4-5 | 9-24 | 6 | 30,659 | Zach Duke | Mike O'Connor | Mike O'Connor | Zach Duke | Chad Cordero | 122 | 168 | -46 |
| 2006-05-09 | vs ARI | 34 | W 3-0 | 10-24 | 6 | 16,961 | Ian Snell | Miguel Batista | Ian Snell | Miguel Batista | Mike Gonzalez | 125 | 168 | -43 |
| 2006-05-10 | vs ARI | 35 | L 4-7 | 10-25 | 6 | 14,509 | Paul Maholm | Brandon Webb | Brandon Webb | Damaso Marte | Jose Valverde | 129 | 175 | -46 |
| 2006-05-12 | vs FLO | 36 | W 12-9 | 11-25 | 6 | 24,990 | Victor Santos | Sergio Mitre | Matt Capps | Todd Wellemeyer | Mike Gonzalez | 141 | 184 | -43 |
| 2006-05-13 | vs FLO | 37 | L 3-4 | 11-26 | 6 | 29,289 | Zach Duke | Scott Olsen | Scott Olsen | Zach Duke | Joe Borowski | 144 | 188 | -44 |
| 2006-05-14 | vs FLO | 38 | L 2-8 | 11-27 | 6 | 15,921 | Ian Snell | Brian Moehler | Brian Moehler | Ian Snell | | 146 | 196 | -50 |
| 2006-05-16 | vs CIN | 39 | W 9-3 | 12-27 | 6 | 14,315 | Paul Maholm | Aaron Harang | Paul Maholm | Aaron Harang | | 155 | 199 | -44 |
| 2006-05-17 | vs CIN | 40 | W 7-2 | 13-27 | 6 | 14,897 | Oliver Perez | Bronson Arroyo | Oliver Perez | Bronson Arroyo | | 162 | 201 | -39 |
| 2006-05-18 | vs CIN | 41 | L 8-9 | 13-28 | 6 | 18,502 | Victor Santos | David Williams | Matt Belisle | Matt Capps | Todd Coffey | 170 | 210 | -40 |
| 2006-05-19 | @ CLE | 42 | L 1-4 | 13-29 | 6 | 32,499 | Zach Duke | CC Sabathia | CC Sabathia | Zach Duke | | 171 | 214 | -43 |
| 2006-05-20 | @ CLE | 43 | W 9-6 | 14-29 | 6 | 30,799 | Ian Snell | Jason Johnson | Ian Snell | Jason Johnson | Mike Gonzalez | 180 | 220 | -40 |
| 2006-05-21 | @ CLE | 44 | L 2-3 | 14-30 | 6 | 31,589 | Paul Maholm | Paul Byrd | Bob Wickman | Mike Gonzalez | | 182 | 223 | -41 |
| 2006-05-22 | @ ARI | 45 | L 3-4 | 14-31 | 6 | 18,103 | Oliver Perez | Orlando Hernandez | Brandon Medders | Damaso Marte | Jose Valverde | 185 | 227 | -42 |
| 2006-05-23 | @ ARI | 46 | L 3-7 | 14-32 | 6 | 19,993 | Victor Santos | Claudio Vargas | Claudio Vargas | Victor Santos | | 188 | 234 | -46 |
| 2006-05-24 | @ ARI | 47 | L 7-8 | 14-33 | 6 | 18,394 | Zach Duke | Miguel Batista | Miguel Batista | Zach Duke | Jose Valverde | 195 | 242 | -47 |
| 2006-05-26 | vs HOU | 48 | W 12-5 | 15-33 | 6 | 29,247 | Ian Snell | Taylor Buchholz | Ian Snell | Taylor Buchholz | | 207 | 247 | -40 |
| 2006-05-27 | vs HOU | 49 | W 8-7 | 16-33 | 6 | 31,878 | Paul Maholm | Wandy Rodriguez | Victor Santos | Mike Gallo | | 215 | 254 | -39 |
| 2006-05-28 | vs HOU | 50 | L 4-5 | 16-34 | 6 | 24,992 | Oliver Perez | Fernando Nieve | Chad Qualls | Salomon Torres | Brad Lidge | 219 | 259 | -40 |
| 2006-05-29 | vs MIL | 51 | W 14-3 | 17-34 | 6 | 17,561 | Zach Duke | Doug Davis | Zach Duke | Doug Davis | | 233 | 262 | -29 |
| 2006-05-30 | vs MIL | 52 | W 12-1 | 18-34 | 6 | 14,300 | Victor Santos | Jorge de la Rosa | Victor Santos | Jorge de la Rosa | | 245 | 263 | -18 |
| 2006-05-31 | vs MIL | 53 | W 6-1 | 19-34 | 6 | 15,434 | Ian Snell | Chris Capuano | Ian Snell | Chris Capuano | | 251 | 264 | -13 |
| 2006-06-01 | vs MIL | 54 | W 4-3 | 20-34 | 6 | 12,899 | Paul Maholm | David Bush | John Grabow | Derrick Turnbow | | 255 | 267 | -12 |
| 2006-06-02 | vs SDN | 55 | L 0-7 | 20-35 | 6 | 20,777 | Oliver Perez | Chan Ho Park | Chan Ho Park | Oliver Perez | | 255 | 274 | -19 |
| 2006-06-03 | vs SDN | 56 | W 6-4 | 21-35 | 6 | 30,639 | Zach Duke | Mike Thompson | Zach Duke | Mike Thompson | Mike Gonzalez | 261 | 278 | -17 |
| 2006-06-04 | vs SDN | 57 | L 0-1 | 21-36 | 6 | 26,857 | Victor Santos | Chris Young | Chris Young | Victor Santos | Trevor Hoffman | 261 | 279 | -18 |
| 2006-06-05 | @ COL | 58 | W 5-2 | 22-36 | 6 | 20,152 | Ian Snell | Aaron Cook | Ian Snell | Aaron Cook | Mike Gonzalez | 266 | 281 | -15 |
| 2006-06-06 | @ COL | 59 | L 4-5 | 22-37 | 6 | 20,277 | Paul Maholm | Jeff Francis | Jeff Francis | Paul Maholm | Brian Fuentes | 270 | 286 | -16 |
| 2006-06-07 | @ COL | 60 | L 9-16 | 22-38 | 6 | 21,509 | Oliver Perez | Josh Fogg | Scott Dohmann | Oliver Perez | | 279 | 302 | -23 |
| 2006-06-08 | @ SFN | 61 | L 4-5 | 22-39 | 6 | 34,540 | Zach Duke | Matt Cain | Armando Benitez | Damaso Marte | | 283 | 307 | -24 |
| 2006-06-09 | @ SFN | 62 | W 3-2 | 23-39 | 6 | 38,766 | Victor Santos | Matt Morris | Victor Santos | Matt Morris | Mike Gonzalez | 286 | 309 | -23 |
| 2006-06-10 | @ SFN | 63 | W 2-0 | 24-39 | 6 | 37,302 | Ian Snell | Noah Lowry | Ian Snell | Noah Lowry | Mike Gonzalez | 288 | 309 | -21 |
| 2006-06-11 | @ SFN | 64 | W 7-5 | 25-39 | 6 | 39,850 | Paul Maholm | Jason Schmidt | Matt Capps | Tim Worrell | Mike Gonzalez | 295 | 314 | -19 |
| 2006-06-13 | vs SLN | 65 | L 1-2 | 25-40 | 6 | 24,443 | Oliver Perez | Chris Carpenter | Chris Carpenter | Oliver Perez | Jason Isringhausen | 296 | 316 | -20 |
| 2006-06-14 | vs SLN | 66 | W 9-7 | 26-40 | 6 | 20,289 | Zach Duke | Sidney Ponson | Zach Duke | Sidney Ponson | Mike Gonzalez | 305 | 323 | -18 |
| 2006-06-15 | vs SLN | 67 | L 5-6 | 26-41 | 6 | 18,248 | Victor Santos | Mark Mulder | Mark Mulder | Victor Santos | Jason Isringhausen | 310 | 329 | -19 |
| 2006-06-16 | vs MIN | 68 | L 2-4 | 26-42 | 6 | 33,025 | Ian Snell | Francisco Liriano | Francisco Liriano | Ian Snell | Joe Nathan | 312 | 333 | -21 |
| 2006-06-17 | vs MIN | 69 | L 3-5 | 26-43 | 6 | 34,085 | Paul Maholm | Boof Bonser | Jesse Crain | Damaso Marte | Joe Nathan | 315 | 338 | -23 |
| 2006-06-18 | vs MIN | 70 | L 2-8 | 26-44 | 6 | 25,104 | Oliver Perez | Johan Santana | Johan Santana | Oliver Perez | | 317 | 346 | -29 |
| 2006-06-19 | vs ARI | 71 | L 4-5 | 26-45 | 6 | 15,032 | Zach Duke | Claudio Vargas | Greg Aquino | Salomon Torres | Jorge Julio | 321 | 351 | -30 |
| 2006-06-20 | @ KCA | 72 | L 6-10 | 26-46 | 6 | 15,906 | Kip Wells | Mark Redman | Mark Redman | Kip Wells | | 327 | 361 | -34 |
| 2006-06-21 | @ KCA | 73 | L 4-6 | 26-47 | 6 | 15,501 | Ian Snell | Mike Wood | Elmer Dessens | Salomon Torres | Ambiorix Burgos | 331 | 367 | -36 |
| 2006-06-22 | @ KCA | 74 | L 7-15 | 26-48 | 6 | 13,153 | Paul Maholm | Scott Elarton | Scott Elarton | Paul Maholm | | 338 | 382 | -44 |
| 2006-06-23 | @ LAN | 75 | L 4-10 | 26-49 | 6 | 55,823 | Oliver Perez | Brett Tomko | Brett Tomko | Oliver Perez | | 342 | 392 | -50 |
| 2006-06-24 | @ LAN | 76 | L 0-7 | 26-50 | 6 | 47,785 | Zach Duke | Aaron Sele | Aaron Sele | Zach Duke | | 342 | 399 | -57 |
| 2006-06-25 | @ LAN | 77 | L 4-7 | 26-51 | 6 | 55,545 | Kip Wells | Brad Penny | Brad Penny | Kip Wells | Takashi Saito | 346 | 406 | -60 |
| 2006-06-27 | vs CHA | 78 | L 2-4 | 26-52 | 6 | 24,976 | Ian Snell | Mark Buehrle | Mark Buehrle | Ian Snell | Bobby Jenks | 348 | 410 | -62 |
| 2006-06-28 | vs CHA | 79 | L 3-4 | 26-53 | 6 | 23,118 | Paul Maholm | Freddy Garcia | Freddy Garcia | Paul Maholm | Bobby Jenks | 351 | 414 | -63 |
| 2006-06-29 | vs CHA | 80 | W 7-6 | 27-53 | 6 | 21,380 | Zach Duke | Jose Contreras | Mike Gonzalez | Cliff Politte | | 358 | 420 | -62 |
| 2006-06-30 | vs DET | 81 | L 6-7 | 27-54 | 6 | 27,318 | Kip Wells | Kenny Rogers | Roman Colon | Kip Wells | Todd Jones | 364 | 427 | -63 |
| 2006-07-01 | vs DET | 82 | W 9-2 | 28-54 | 6 | 37,111 | Tom Gorzelanny | Jeremy Bonderman | Matt Capps | Jason Grilli | | 373 | 429 | -56 |
| 2006-07-02 | vs DET | 83 | L 8-9 | 28-55 | 6 | 28,136 | Ian Snell | Zach Miner | Zach Miner | Ian Snell | Todd Jones | 381 | 438 | -57 |
| 2006-07-03 | @ NYN | 84 | W 11-1 | 29-55 | 6 | 54,111 | Paul Maholm | John Maine | Paul Maholm | John Maine | | 392 | 439 | -47 |
| 2006-07-04 | @ NYN | 85 | L 6-7 | 29-56 | 6 | 38,487 | Zach Duke | Tom Glavine | Duaner Sanchez | Roberto Hernandez | Billy Wagner | 398 | 446 | -48 |
| 2006-07-05 | @ NYN | 86 | L 0-5 | 29-57 | 6 | 40,360 | Kip Wells | Orlando Hernandez | Orlando Hernandez | Kip Wells | | 398 | 451 | -53 |
| 2006-07-06 | @ NYN | 87 | L 5-7 | 29-58 | 6 | 39,743 | Tom Gorzelanny | Steve Trachsel | Steve Trachsel | Tom Gorzelanny | Billy Wagner | 403 | 458 | -55 |
| 2006-07-07 | @ PHI | 88 | W 3-2 | 30-58 | 6 | 45,025 | Ian Snell | Jon Lieber | Ian Snell | Jon Lieber | Mike Gonzalez | 406 | 460 | -54 |
| 2006-07-08 | @ PHI | 89 | L 2-6 | 30-59 | 6 | 37,462 | Paul Maholm | Cory Lidle | Cory Lidle | Paul Maholm | | 408 | 466 | -58 |
| 2006-07-09 | @ PHI | 90 | L 3-8 | 30-60 | 6 | 32,527 | Zach Duke | Cole Hamels | Cole Hamels | Zach Duke | | 411 | 474 | -63 |
| 2006-07-14 | vs WAS | 91 | W 7-4 | 31-60 | 6 | 26,720 | Zach Duke | Ramon Ortiz | Zach Duke | Ramon Ortiz | Mike Gonzalez | 418 | 478 | -60 |
| 2006-07-15 | vs WAS | 92 | W 7-6 | 32-60 | 6 | 32,626 | Ian Snell | Pedro Astacio | Mike Gonzalez | Roy Corcoran | | 425 | 484 | -59 |
| 2006-07-16 | vs WAS | 93 | L 4-8 | 32-61 | 6 | 18,908 | Paul Maholm | Livan Hernandez | Mike Stanton | Roberto Hernandez | | 429 | 492 | -63 |
| 2006-07-17 | vs COL | 94 | W 3-1 | 33-61 | 6 | 18,835 | Kip Wells | Byung-Hyun Kim | John Grabow | Byung-Hyun Kim | Matt Capps | 432 | 493 | -61 |
| 2006-07-18 | vs COL | 95 | L 4-13 | 33-62 | 6 | 20,086 | Tom Gorzelanny | Jeff Francis | Jeff Francis | Tom Gorzelanny | | 436 | 506 | -70 |
| 2006-07-19 | vs COL | 96 | W 6-5 | 34-62 | 6 | 19,881 | Zach Duke | Jason Jennings | Zach Duke | Jason Jennings | Mike Gonzalez | 442 | 511 | -69 |
| 2006-07-20 | @ FLO | 97 | W 5-3 | 35-62 | 6 | 9,139 | Ian Snell | Josh Johnson | Salomon Torres | Randy Messenger | Mike Gonzalez | 447 | 514 | -67 |
| 2006-07-21 | @ FLO | 98 | L 1-4 | 35-63 | 6 | 11,357 | Paul Maholm | Scott Olsen | Scott Olsen | Paul Maholm | Joe Borowski | 448 | 518 | -70 |
| 2006-07-22 | @ FLO | 99 | L 0-5 | 35-64 | 6 | 15,291 | Kip Wells | Ricky Nolasco | Ricky Nolasco | Kip Wells | | 448 | 523 | -75 |
| 2006-07-23 | @ FLO | 100 | L 4-5 | 35-65 | 6 | 11,468 | Tom Gorzelanny | Dontrelle Willis | Joe Borowski | Mike Gonzalez | | 452 | 528 | -76 |
| 2006-07-24 | @ MIL | 101 | L 8-12 | 35-66 | 6 | 30,252 | Zach Duke | Doug Davis | Doug Davis | Zach Duke | | 460 | 540 | -80 |
| 2006-07-25 | @ MIL | 102 | W 6-1 | 36-66 | 6 | 35,923 | Ian Snell | Ben Sheets | Ian Snell | David Bush | | 466 | 541 | -75 |
| 2006-07-26 | @ MIL | 103 | W 8-4 | 37-66 | 6 | 37,678 | Paul Maholm | Chris Capuano | Paul Maholm | Chris Capuano | | 474 | 545 | -71 |
| 2006-07-28 | vs SFN | 104 | W 3-0 | 38-66 | 6 | 38,092 | Kip Wells | Jason Schmidt | Kip Wells | Jason Schmidt | Mike Gonzalez | 477 | 545 | -68 |
| 2006-07-29 | vs SFN | 105 | W 4-3 | 39-66 | 6 | 38,373 | Tom Gorzelanny | Jamey Wright | Tom Gorzelanny | Jamey Wright | Mike Gonzalez | 481 | 548 | -67 |
| 2006-07-30 | vs SFN | 106 | W 2-1 | 40-66 | 6 | 26,516 | Zach Duke | Matt Morris | John Grabow | Steve Kline | | 483 | 549 | -66 |
| 2006-08-01 | vs ATL | 107 | L 2-4 | 40-67 | 6 | 22,145 | Ian Snell | John Smoltz | John Smoltz | Ian Snell | Bob Wickman | 485 | 553 | -68 |
| 2006-08-02 | vs ATL | 108 | L 2-3 | 40-68 | 6 | 21,064 | Paul Maholm | Horacio Ramirez | Tyler Yates | Salomon Torres | Bob Wickman | 487 | 556 | -69 |
| 2006-08-03 | vs ATL | 109 | W 3-2 | 41-68 | 6 | 17,324 | Shawn Chacon | Tim Hudson | Shawn Chacon | Tim Hudson | Mike Gonzalez | 490 | 558 | -68 |
| 2006-08-04 | @ CHN | 110 | W 6-0 | 42-68 | 6 | 39,973 | Tom Gorzelanny | Carlos Zambrano | Tom Gorzelanny | Carlos Zambrano | | 496 | 558 | -62 |
| 2006-08-05 | @ CHN | 111 | L 5-7 | 42-69 | 6 | 41,007 | Zach Duke | Mark Prior | Mark Prior | Zach Duke | Ryan Dempster | 501 | 565 | -64 |
| 2006-08-06 | @ CHN | 112 | L 1-6 | 42-70 | 6 | 40,320 | Ian Snell | Rich Hill | Rich Hill | Ian Snell | | 502 | 571 | -69 |
| 2006-08-08 | @ HOU | 113 | L 1-3 | 42-71 | 6 | 38,856 | Paul Maholm | Brandon Backe | Brandon Backe | Paul Maholm | Brad Lidge | 503 | 574 | -71 |
| 2006-08-09 | @ HOU | 114 | L 1-14 | 42-72 | 6 | 31,077 | Shawn Chacon | Roy Oswalt | Roy Oswalt | Shawn Chacon | | 504 | 588 | -84 |
| 2006-08-10 | @ HOU | 115 | L 2-5 | 42-73 | 6 | 41,476 | Tom Gorzelanny | Roger Clemens | Roger Clemens | Tom Gorzelanny | | 506 | 593 | -87 |
| 2006-08-11 | vs SLN | 116 | W 7-1 | 43-73 | 6 | 30,516 | Zach Duke | Jeff Suppan | Zach Duke | Jeff Suppan | | 513 | 594 | -81 |
| 2006-08-12 | vs SLN | 117 | W 3-2 | 44-73 | 6 | 35,037 | Ian Snell | Jeff Weaver | Ian Snell | Jeff Weaver | Mike Gonzalez | 516 | 596 | -80 |
| 2006-08-13 | vs SLN | 118 | W 7-0 | 45-73 | 6 | 27,101 | Paul Maholm | Jason Marquis | Paul Maholm | Jason Marquis | | 523 | 596 | -73 |
| 2006-08-14 | vs MIL | 119 | W 4-2 | 46-73 | 6 | 16,279 | Victor Santos | David Bush | Victor Santos | David Bush | Mike Gonzalez | 527 | 598 | -71 |
| 2006-08-15 | vs MIL | 120 | L 3-6 | 46-74 | 6 | 17,877 | Tom Gorzelanny | Doug Davis | Doug Davis | Damaso Marte | Francisco Cordero | 530 | 604 | -74 |
| 2006-08-16 | vs MIL | 121 | L 2-5 | 46-75 | 6 | 14,901 | Zach Duke | Chris Capuano | Geremi Gonzalez | Damaso Marte | Francisco Cordero | 532 | 609 | -77 |
| 2006-08-18 | @ CIN | 122 | W 7-3 | 47-75 | 6 | 31,718 | Ian Snell | Chris Michalak | Ian Snell | Chris Michalak | | 539 | 612 | -73 |
| 2006-08-19 | @ CIN | 123 | L 7-14 | 47-76 | 6 | 34,245 | Paul Maholm | Eric Milton | Ryan Franklin | Salomon Torres | | 546 | 626 | -80 |
| 2006-08-20 | @ CIN | 124 | L 1-5 | 47-77 | 6 | 29,935 | Victor Santos | Aaron Harang | Aaron Harang | Victor Santos | | 547 | 631 | -84 |
| 2006-08-21 | @ ATL | 125 | L 0-3 | 47-78 | 6 | 21,898 | Zach Duke | John Smoltz | John Smoltz | Zach Duke | Bob Wickman | 547 | 634 | -87 |
| 2006-08-22 | @ ATL | 126 | W 5-3 | 48-78 | 6 | 21,830 | Shawn Chacon | Oscar Villarreal | Damaso Marte | Danys Baez | Mike Gonzalez | 552 | 637 | -85 |
| 2006-08-23 | @ ATL | 127 | W 5-4 | 49-78 | 6 | 23,082 | Ian Snell | Tim Hudson | Matt Capps | Chad Paronto | Mike Gonzalez | 557 | 641 | -84 |
| 2006-08-24 | vs HOU | 128 | W 5-3 | 50-78 | 6 | 32,345 | Paul Maholm | Wandy Rodriguez | Paul Maholm | Wandy Rodriguez | Mike Gonzalez | 562 | 644 | -82 |
| 2006-08-25 | vs HOU | 129 | L 1-5 | 50-79 | 6 | 37,009 | Victor Santos | Roger Clemens | Roger Clemens | Victor Santos | | 563 | 649 | -86 |
| 2006-08-26 | vs HOU | 130 | L 4-7 | 50-80 | 6 | 37,190 | Zach Duke | Andy Pettitte | Andy Pettitte | Zach Duke | Brad Lidge | 567 | 656 | -89 |
| 2006-08-27 | vs HOU | 131 | L 1-13 | 50-81 | 6 | 19,459 | Shawn Chacon | Jason Hirsh | Jason Hirsh | Shawn Chacon | | 568 | 669 | -101 |
| 2006-08-28 | vs CHN | 132 | W 11-6 | 51-81 | 6 | 12,666 | Ian Snell | Angel Guzman | Ian Snell | Angel Guzman | | 579 | 675 | -96 |
| 2006-08-29 | vs CHN | 133 | W 7-6 | 52-81 | 6 | 14,618 | Paul Maholm | Carlos Zambrano | Matt Capps | Ryan Dempster | | 586 | 681 | -95 |
| 2006-08-30 | vs CHN | 134 | W 10-9 | 53-81 | 6 | 12,730 | Victor Santos | Juan Mateo | Marty McLeary | Ryan Dempster | | 596 | 690 | -94 |
| 2006-09-01 | @ SLN | 135 | L 1-3 | 53-82 | 6 | 42,091 | Zach Duke | Chris Carpenter | Chris Carpenter | Zach Duke | | 597 | 693 | -96 |
| 2006-09-02 | @ SLN | 136 | W 1-0 | 54-82 | 6 | 41,466 | Shawn Chacon | Jeff Weaver | Matt Capps | Jeff Weaver | Salomon Torres | 598 | 693 | -95 |
| 2006-09-03 | @ SLN | 137 | L 3-6 | 54-83 | 6 | 42,205 | Ian Snell | Anthony Reyes | Anthony Reyes | Ian Snell | | 601 | 699 | -98 |
| 2006-09-04 | @ CHN | 138 | W 5-4 | 55-83 | 6 | 37,994 | Paul Maholm | Carlos Zambrano | Paul Maholm | Carlos Zambrano | Salomon Torres | 606 | 703 | -97 |
| 2006-09-05 | @ CHN | 139 | W 6-5 | 56-83 | 5 | 31,494 | Victor Santos | Juan Mateo | John Grabow | Ryan Dempster | Salomon Torres | 612 | 708 | -96 |
| 2006-09-06 | @ CHN | 140 | L 2-7 | 56-84 | 6 | 32,557 | Zach Duke | Rich Hill | Michael Wuertz | John Grabow | | 614 | 715 | -101 |
| 2006-09-07 | @ CHN | 141 | W 7-5 | 57-84 | 5 | 27,105 | Shawn Chacon | Sean Marshall | Jonah Bayliss | Scott Eyre | Salomon Torres | 621 | 720 | -99 |
| 2006-09-08 | @ CIN | 142 | L 1-9 | 57-85 | 5 | 17,631 | Ian Snell | Kyle Lohse | Kyle Lohse | Ian Snell | | 622 | 729 | -107 |
| 2006-09-09 | @ CIN | 143 | W 7-4 | 58-85 | 5 | 25,038 | Paul Maholm | Aaron Harang | Matt Capps | Todd Coffey | Salomon Torres | 629 | 733 | -104 |
| 2006-09-10 | @ CIN | 144 | L 2-4 | 58-86 | 5 | 20,731 | Shane Youman | Bronson Arroyo | Bronson Arroyo | Shane Youman | Scott Schoeneweis | 631 | 737 | -106 |
| 2006-09-11 | vs MIL | 145 | W 4-3 | 59-86 | 5 | 13,643 | Zach Duke | Doug Davis | Zach Duke | Doug Davis | Salomon Torres | 635 | 740 | -105 |
| 2006-09-13 | vs MIL | 146 | W 6-3 | 60-87 | 5 | 0 | Ian Snell | Chris Capuano | Ian Snell | Chris Capuano | Salomon Torres | 641 | 743 | -102 |
| 2006-09-13 | vs MIL | 147 | L 1-2 | 60-87 | 5 | 11,627 | Shawn Chacon | Ben Sheets | Ben Sheets | Shawn Chacon | Francisco Cordero | 642 | 745 | -103 |
| 2006-09-15 | vs NYN | 148 | W 5-3 | 61-87 | 5 | 24,410 | Paul Maholm | Pedro Martinez | Paul Maholm | Pedro Martinez | Salomon Torres | 647 | 748 | -101 |
| 2006-09-16 | vs NYN | 149 | W 3-2 | 62-87 | 5 | 37,623 | Tom Gorzelanny | Orlando Hernandez | Matt Capps | Aaron Heilman | | 650 | 750 | -100 |
| 2006-09-17 | vs NYN | 150 | W 3-0 | 63-87 | 5 | 34,866 | Zach Duke | John Maine | Zach Duke | John Maine | Salomon Torres | 653 | 750 | -97 |
| 2006-09-19 | @ LAN | 151 | W 10-6 | 64-87 | 5 | 43,734 | Ian Snell | Hong-Chih Kuo | Ian Snell | Hong-Chih Kuo | | 663 | 756 | -93 |
| 2006-09-20 | @ LAN | 152 | W 6-4 | 65-87 | 5 | 46,319 | Shawn Chacon | Greg Maddux | Shawn Chacon | Greg Maddux | Salomon Torres | 669 | 760 | -91 |
| 2006-09-21 | @ LAN | 153 | L 2-5 | 65-88 | 5 | 48,567 | Shane Youman | Chad Billingsley | Chad Billingsley | Shane Youman | Takashi Saito | 671 | 765 | -94 |
| 2006-09-22 | @ SDN | 154 | L 2-6 | 65-89 | 5 | 40,077 | Tom Gorzelanny | Chris Young | Chris Young | Tom Gorzelanny | | 673 | 771 | -98 |
| 2006-09-23 | @ SDN | 155 | L 1-2 | 65-90 | 5 | 43,168 | Zach Duke | Jake Peavy | Jake Peavy | Zach Duke | Trevor Hoffman | 674 | 773 | -99 |
| 2006-09-24 | @ SDN | 156 | L 1-2 | 65-91 | 5 | 41,932 | Marty McLeary | Clay Hensley | Clay Hensley | Juan Perez | Trevor Hoffman | 675 | 775 | -100 |
| 2006-09-26 | vs HOU | 157 | L 4-7 | 65-92 | 5 | 17,141 | Ian Snell | Andy Pettitte | Andy Pettitte | Ian Snell | | 679 | 782 | -103 |
| 2006-09-27 | vs HOU | 158 | L 6-7 | 65-93 | 5 | 16,352 | Shawn Chacon | Jason Hirsh | Chris Sampson | Jonah Bayliss | Trever Miller | 685 | 789 | -104 |
| 2006-09-28 | vs HOU | 159 | L 0-3 | 65-94 | 6 | 12,671 | Tom Gorzelanny | Roy Oswalt | Roy Oswalt | Tom Gorzelanny | Brad Lidge | 685 | 792 | -107 |
| 2006-09-29 | vs CIN | 160 | L 2-5 | 65-95 | 6 | 27,033 | Zach Duke | Aaron Harang | Aaron Harang | Zach Duke | | 687 | 797 | -110 |
| 2006-09-30 | vs CIN | 161 | W 3-0 | 66-95 | 5 | 35,514 | Marty McLeary | Bronson Arroyo | Marty McLeary | Bronson Arroyo | Salomon Torres | 690 | 797 | -107 |
| 2006-10-01 | vs CIN | 162 | W 1-0 | 67-95 | 5 | 25,004 | Shane Youman | Matt Belisle | Matt Capps | Todd Coffey | Salomon Torres | 691 | 797 | -106 |