| 2006-04-03 | @ LAN | 1 | W 11-10 | 1-0 | 1 | 56,000 | Tim Hudson | Derek Lowe | Oscar Villarreal | Derek Lowe | Chris Reitsma | 11 | 10 | 1 |
| 2006-04-04 | @ LAN | 2 | L 4-5 | 1-1 | 2 | 36,249 | John Smoltz | Brad Penny | Brad Penny | John Smoltz | Danys Baez | 15 | 15 | 0 |
| 2006-04-05 | @ LAN | 3 | W 9-8 | 2-1 | 1 | 35,292 | Horacio Ramirez | Odalis Perez | Oscar Villarreal | Franquelis Osoria | Chris Reitsma | 24 | 23 | 1 |
| 2006-04-06 | @ SFN | 4 | L 4-6 | 2-2 | 2 | 42,795 | Jorge Sosa | Noah Lowry | Jeff Fassero | Jorge Sosa | Tim Worrell | 28 | 29 | -1 |
| 2006-04-07 | @ SFN | 5 | W 14-6 | 3-2 | 2 | 39,737 | Kyle Davies | Matt Cain | Mike Remlinger | Tyler Walker | | 42 | 35 | 7 |
| 2006-04-08 | @ SFN | 6 | L 6-12 | 3-3 | 2 | 39,050 | Tim Hudson | Jamey Wright | Jamey Wright | Tim Hudson | | 48 | 47 | 1 |
| 2006-04-09 | @ SFN | 7 | L 5-6 | 3-4 | 2 | 37,321 | John Smoltz | Jason Schmidt | Tim Worrell | Chris Reitsma | | 53 | 53 | 0 |
| 2006-04-10 | vs PHI | 8 | W 5-3 | 4-4 | 2 | 47,332 | John Thomson | Brett Myers | Oscar Villarreal | Ryan Franklin | Chris Reitsma | 58 | 56 | 2 |
| 2006-04-12 | vs PHI | 9 | L 5-7 | 4-5 | 2 | 37,107 | Jorge Sosa | Cory Lidle | Cory Lidle | Jorge Sosa | Tom Gordon | 63 | 63 | 0 |
| 2006-04-13 | vs PHI | 10 | L 6-7 | 4-6 | 2 | 22,911 | Kyle Davies | Gavin Floyd | Gavin Floyd | Kyle Davies | Tom Gordon | 69 | 70 | -1 |
| 2006-04-14 | vs SDN | 11 | W 5-4 | 5-6 | 2 | 36,406 | Tim Hudson | Chan Ho Park | Oscar Villarreal | Scott Linebrink | Chris Reitsma | 74 | 74 | 0 |
| 2006-04-15 | vs SDN | 12 | W 2-0 | 6-6 | 2 | 40,151 | John Smoltz | Jake Peavy | John Smoltz | Jake Peavy | | 76 | 74 | 2 |
| 2006-04-16 | vs SDN | 13 | L 3-4 | 6-7 | 2 | 24,589 | John Thomson | Woody Williams | Scott Linebrink | Mike Remlinger | Trevor Hoffman | 79 | 78 | 1 |
| 2006-04-17 | @ NYN | 14 | L 3-4 | 6-8 | 2 | 36,867 | Jorge Sosa | Pedro Martinez | Pedro Martinez | Jorge Sosa | Billy Wagner | 82 | 82 | 0 |
| 2006-04-18 | @ NYN | 15 | W 7-1 | 7-8 | 2 | 30,322 | Kyle Davies | Victor Zambrano | Kyle Davies | Victor Zambrano | | 89 | 83 | 6 |
| 2006-04-19 | @ NYN | 16 | W 2-1 | 8-8 | 2 | 40,861 | Tim Hudson | Tom Glavine | Tim Hudson | Tom Glavine | | 91 | 84 | 7 |
| 2006-04-21 | @ WAS | 17 | L 3-7 | 8-9 | 2 | 24,597 | John Smoltz | John Patterson | Mike Stanton | Lance Cormier | | 94 | 91 | 3 |
| 2006-04-23 | @ WAS | 18 | W 3-1 | 9-9 | 2 | 21,569 | John Thomson | Tony Armas | Lance Cormier | Gary Majewski | Mike Remlinger | 97 | 92 | 5 |
| 2006-04-24 | @ MIL | 19 | L 2-3 | 9-10 | 2 | 11,660 | Kyle Davies | Chris Capuano | Chris Capuano | Kyle Davies | Derrick Turnbow | 99 | 95 | 4 |
| 2006-04-25 | @ MIL | 20 | L 2-4 | 9-11 | 2 | 16,276 | Tim Hudson | Tomo Ohka | Tomo Ohka | Tim Hudson | Derrick Turnbow | 101 | 99 | 2 |
| 2006-04-26 | @ MIL | 21 | L 4-5 | 9-12 | 3 | 18,511 | Jorge Sosa | Ben Sheets | Ben Sheets | Jorge Sosa | Derrick Turnbow | 105 | 104 | 1 |
| 2006-04-28 | vs NYN | 22 | L 2-5 | 9-13 | 2 | 45,389 | John Smoltz | Pedro Martinez | Pedro Martinez | John Smoltz | Billy Wagner | 107 | 109 | -2 |
| 2006-04-29 | vs NYN | 23 | L 0-1 | 9-14 | 2 | 46,387 | John Thomson | Tom Glavine | Tom Glavine | John Thomson | Billy Wagner | 107 | 110 | -3 |
| 2006-04-30 | vs NYN | 24 | W 8-5 | 10-14 | 2 | 35,245 | Kyle Davies | Steve Trachsel | Kyle Davies | Steve Trachsel | Chris Reitsma | 115 | 115 | 0 |
| 2006-05-01 | vs COL | 25 | W 2-0 | 11-14 | 2 | 19,212 | Tim Hudson | Jason Jennings | Tim Hudson | Jason Jennings | | 117 | 115 | 2 |
| 2006-05-02 | vs COL | 26 | W 5-4 | 12-14 | 2 | 22,813 | Jorge Sosa | Aaron Cook | Lance Cormier | Ray King | Chris Reitsma | 122 | 119 | 3 |
| 2006-05-03 | @ PHI | 27 | L 4-5 | 12-15 | 3 | 26,443 | John Smoltz | Brett Myers | Rheal Cormier | Mike Remlinger | Tom Gordon | 126 | 124 | 2 |
| 2006-05-04 | @ PHI | 28 | L 3-6 | 12-16 | 3 | 24,842 | John Thomson | Cory Lidle | Cory Lidle | John Thomson | Arthur Rhodes | 129 | 130 | -1 |
| 2006-05-05 | @ NYN | 29 | L 7-8 | 12-17 | 3 | 47,720 | Kyle Davies | Steve Trachsel | Jorge Julio | Jorge Sosa | | 136 | 138 | -2 |
| 2006-05-06 | @ NYN | 30 | L 5-6 | 12-18 | 3 | 48,369 | Tim Hudson | Victor Zambrano | Bartolome Fortunato | Tim Hudson | Jorge Julio | 141 | 144 | -3 |
| 2006-05-07 | @ NYN | 31 | W 13-3 | 13-18 | 3 | 48,100 | John Smoltz | Jose Lima | John Smoltz | Jose Lima | | 154 | 147 | 7 |
| 2006-05-09 | @ FLO | 32 | W 10-2 | 14-18 | 3 | 6,079 | John Thomson | Brian Moehler | John Thomson | Brian Moehler | | 164 | 149 | 15 |
| 2006-05-10 | @ FLO | 33 | L 3-11 | 14-19 | 3 | 6,299 | Kyle Davies | Josh Johnson | Josh Johnson | Kyle Davies | | 167 | 160 | 7 |
| 2006-05-11 | @ FLO | 34 | W 9-1 | 15-19 | 3 | 8,717 | Tim Hudson | Dontrelle Willis | Tim Hudson | Dontrelle Willis | | 176 | 161 | 15 |
| 2006-05-12 | vs WAS | 35 | W 6-2 | 16-19 | 3 | 31,818 | John Smoltz | Ramon Ortiz | John Smoltz | Ramon Ortiz | | 182 | 163 | 19 |
| 2006-05-13 | vs WAS | 36 | W 8-5 | 17-19 | 3 | 37,040 | Jorge Sosa | Mike O'Connor | Chris Reitsma | Chad Cordero | | 190 | 168 | 22 |
| 2006-05-14 | vs WAS | 37 | L 1-8 | 17-20 | 3 | 31,062 | John Thomson | Tony Armas | Tony Armas | John Thomson | | 191 | 176 | 15 |
| 2006-05-15 | vs FLO | 38 | W 11-8 | 18-20 | 3 | 19,254 | Kyle Davies | Josh Johnson | Oscar Villarreal | Randy Messenger | Chris Reitsma | 202 | 184 | 18 |
| 2006-05-16 | vs FLO | 39 | W 4-3 | 19-20 | 3 | 22,427 | Tim Hudson | Dontrelle Willis | Macay McBride | Joe Borowski | | 206 | 187 | 19 |
| 2006-05-17 | vs FLO | 40 | W 6-4 | 20-20 | 3 | 25,647 | John Smoltz | Ricky Nolasco | Oscar Villarreal | Randy Messenger | | 212 | 191 | 21 |
| 2006-05-18 | vs FLO | 41 | W 9-1 | 21-20 | 3 | 29,996 | Jorge Sosa | Scott Olsen | Jorge Sosa | Scott Olsen | | 221 | 192 | 29 |
| 2006-05-19 | @ ARI | 42 | L 9-10 | 21-21 | 3 | 25,056 | John Thomson | Miguel Batista | Jose Valverde | Chris Reitsma | | 230 | 202 | 28 |
| 2006-05-20 | @ ARI | 43 | L 0-13 | 21-22 | 3 | 35,382 | Travis Smith | Brandon Webb | Brandon Webb | Travis Smith | | 230 | 215 | 15 |
| 2006-05-21 | @ ARI | 44 | W 2-1 | 22-22 | 3 | 33,102 | Tim Hudson | Juan Cruz | Tim Hudson | Juan Cruz | Macay McBride | 232 | 216 | 16 |
| 2006-05-22 | @ SDN | 45 | W 3-1 | 23-22 | 3 | 25,869 | John Smoltz | Jake Peavy | John Smoltz | Jake Peavy | Chris Reitsma | 235 | 217 | 18 |
| 2006-05-23 | @ SDN | 46 | L 1-2 | 23-23 | 3 | 25,315 | Jorge Sosa | Mike Thompson | Mike Thompson | Jorge Sosa | Trevor Hoffman | 236 | 219 | 17 |
| 2006-05-24 | @ SDN | 47 | W 10-6 | 24-23 | 3 | 23,740 | John Thomson | Chris Young | John Thomson | Chris Young | | 246 | 225 | 21 |
| 2006-05-26 | @ CHN | 48 | W 6-5 | 25-23 | 2 | 40,865 | Tim Hudson | Carlos Zambrano | Mike Remlinger | Ryan Dempster | Ken Ray | 252 | 230 | 22 |
| 2006-05-27 | @ CHN | 49 | W 2-1 | 26-23 | 2 | 41,526 | Horacio Ramirez | Sean Marshall | Horacio Ramirez | Sean Marshall | Mike Remlinger | 254 | 231 | 23 |
| 2006-05-28 | @ CHN | 50 | W 13-12 | 27-23 | 2 | 41,698 | John Smoltz | Jae Kuk Ryu | Oscar Villarreal | Scott Eyre | Ken Ray | 267 | 243 | 24 |
| 2006-05-29 | vs LAN | 51 | L 5-12 | 27-24 | 2 | 41,825 | John Thomson | Brad Penny | Joe Beimel | John Thomson | | 272 | 255 | 17 |
| 2006-05-30 | vs LAN | 52 | L 3-8 | 27-25 | 3 | 29,517 | Jorge Sosa | Aaron Sele | Danys Baez | Mike Remlinger | | 275 | 263 | 12 |
| 2006-05-31 | vs LAN | 53 | W 9-3 | 28-25 | 2 | 28,880 | Tim Hudson | Brett Tomko | Tim Hudson | Brett Tomko | | 284 | 266 | 18 |
| 2006-06-01 | vs ARI | 54 | L 1-2 | 28-26 | 2 | 23,376 | Horacio Ramirez | Juan Cruz | Juan Cruz | Horacio Ramirez | Jorge Julio | 285 | 268 | 17 |
| 2006-06-03 | vs ARI | 55 | L 2-4 | 28-28 | 3 | 27,126 | John Smoltz | Enrique Gonzalez | Enrique Gonzalez | John Smoltz | Jorge Julio | 287 | 272 | 15 |
| 2006-06-03 | vs ARI | 56 | L 9-13 | 28-28 | 3 | 40,212 | John Thomson | Claudio Vargas | Claudio Vargas | John Thomson | | 296 | 285 | 11 |
| 2006-06-04 | vs ARI | 57 | L 3-9 | 28-29 | 3 | 29,141 | Jorge Sosa | Miguel Batista | Miguel Batista | Jorge Sosa | | 299 | 294 | 5 |
| 2006-06-05 | vs WAS | 58 | L 4-5 | 28-30 | 3 | 20,702 | Tim Hudson | Livan Hernandez | Livan Hernandez | Tim Hudson | Chad Cordero | 303 | 299 | 4 |
| 2006-06-06 | vs WAS | 59 | W 5-3 | 29-30 | 3 | 23,497 | Horacio Ramirez | Shawn Hill | Horacio Ramirez | Shawn Hill | Ken Ray | 308 | 302 | 6 |
| 2006-06-07 | vs WAS | 60 | L 2-5 | 29-31 | 3 | 32,001 | John Smoltz | Ramon Ortiz | Ramon Ortiz | John Smoltz | Chad Cordero | 310 | 307 | 3 |
| 2006-06-08 | @ HOU | 61 | L 4-7 | 29-32 | 3 | 35,752 | John Thomson | Andy Pettitte | Andy Pettitte | John Thomson | Brad Lidge | 314 | 314 | 0 |
| 2006-06-09 | @ HOU | 62 | L 2-7 | 29-33 | 3 | 37,097 | Jorge Sosa | Fernando Nieve | Fernando Nieve | Jorge Sosa | | 316 | 321 | -5 |
| 2006-06-10 | @ HOU | 63 | W 4-2 | 30-33 | 3 | 41,808 | Tim Hudson | Taylor Buchholz | Tim Hudson | Taylor Buchholz | Ken Ray | 320 | 323 | -3 |
| 2006-06-11 | @ HOU | 64 | L 4-14 | 30-34 | 3 | 39,523 | Horacio Ramirez | Wandy Rodriguez | Wandy Rodriguez | Horacio Ramirez | | 324 | 337 | -13 |
| 2006-06-13 | @ FLO | 65 | L 1-4 | 30-35 | 3 | 6,940 | John Smoltz | Josh Johnson | Josh Johnson | John Smoltz | Joe Borowski | 325 | 341 | -16 |
| 2006-06-14 | @ FLO | 66 | L 5-6 | 30-36 | 3 | 8,097 | John Thomson | Dontrelle Willis | Taylor Tankersley | Oscar Villarreal | | 330 | 347 | -17 |
| 2006-06-15 | @ FLO | 67 | L 2-3 | 30-37 | 3 | 7,162 | Jorge Sosa | Ricky Nolasco | Ricky Nolasco | Jorge Sosa | Joe Borowski | 332 | 350 | -18 |
| 2006-06-16 | vs BOS | 68 | L 1-4 | 30-38 | 3 | 51,038 | Tim Hudson | Jon Lester | Jon Lester | Tim Hudson | Jonathan Papelbon | 333 | 354 | -21 |
| 2006-06-17 | vs BOS | 69 | L 3-5 | 30-39 | 4 | 49,364 | Lance Cormier | Josh Beckett | Josh Beckett | Lance Cormier | Jonathan Papelbon | 336 | 359 | -23 |
| 2006-06-18 | vs BOS | 70 | L 7-10 | 30-40 | 5 | 48,826 | John Smoltz | Curt Schilling | Rudy Seanez | Macay McBride | Jonathan Papelbon | 343 | 369 | -26 |
| 2006-06-20 | vs TOR | 71 | L 5-6 | 30-41 | 5 | 26,915 | Jorge Sosa | Josh Towers | Scott Schoeneweis | Tyler Yates | B.J. Ryan | 348 | 375 | -27 |
| 2006-06-21 | vs TOR | 72 | L 3-6 | 30-42 | 5 | 26,232 | Tim Hudson | Ted Lilly | Ted Lilly | Tim Hudson | B.J. Ryan | 351 | 381 | -30 |
| 2006-06-22 | vs TOR | 73 | L 2-3 | 30-43 | 5 | 26,829 | Horacio Ramirez | A.J. Burnett | Ty Taubenheim | Mike Remlinger | B.J. Ryan | 353 | 384 | -31 |
| 2006-06-23 | @ TBA | 74 | W 4-3 | 31-43 | 5 | 21,280 | John Smoltz | Casey Fossum | Jorge Sosa | Chad Harville | | 357 | 387 | -30 |
| 2006-06-24 | @ TBA | 75 | L 2-3 | 31-44 | 5 | 26,686 | Lance Cormier | Tim Corcoran | Tim Corcoran | Lance Cormier | Chad Harville | 359 | 390 | -31 |
| 2006-06-25 | @ TBA | 76 | W 4-1 | 32-44 | 5 | 20,556 | Chuck James | Mark Hendrickson | Chuck James | Mark Hendrickson | Jorge Sosa | 363 | 391 | -28 |
| 2006-06-26 | @ NYA | 77 | L 2-5 | 32-45 | 5 | 54,226 | Tim Hudson | Randy Johnson | Randy Johnson | Tim Hudson | Mariano Rivera | 365 | 396 | -31 |
| 2006-06-27 | @ NYA | 78 | W 5-2 | 33-45 | 4 | 53,763 | Horacio Ramirez | Jaret Wright | Horacio Ramirez | Jaret Wright | | 370 | 398 | -28 |
| 2006-06-28 | @ NYA | 79 | L 3-4 | 33-46 | 4 | 54,186 | John Smoltz | Chien-Ming Wang | Ron Villone | Jorge Sosa | | 373 | 402 | -29 |
| 2006-06-30 | vs BAL | 80 | W 5-3 | 34-46 | 4 | 34,581 | Chuck James | Daniel Cabrera | Chuck James | Kurt Birkins | Jorge Sosa | 378 | 405 | -27 |
| 2006-07-01 | vs BAL | 81 | L 4-7 | 34-47 | 4 | 38,414 | Tim Hudson | Russ Ortiz | Kurt Birkins | Tim Hudson | | 382 | 412 | -30 |
| 2006-07-02 | vs BAL | 82 | W 10-3 | 35-47 | 4 | 27,693 | Horacio Ramirez | Kris Benson | Horacio Ramirez | Kris Benson | | 392 | 415 | -23 |
| 2006-07-03 | vs SLN | 83 | W 6-3 | 36-47 | 4 | 40,011 | John Smoltz | Anthony Reyes | John Smoltz | Anthony Reyes | Jorge Sosa | 398 | 418 | -20 |
| 2006-07-04 | vs SLN | 84 | L 3-6 | 36-48 | 5 | 47,514 | John Thomson | Chris Carpenter | Chris Carpenter | John Thomson | Jason Isringhausen | 401 | 424 | -23 |
| 2006-07-05 | vs SLN | 85 | W 14-4 | 37-48 | 4 | 28,705 | Chuck James | Jeff Suppan | Chuck James | Jeff Suppan | | 415 | 428 | -13 |
| 2006-07-06 | vs CIN | 86 | W 8-7 | 38-48 | 3 | 28,446 | Tim Hudson | Joe Mays | Ken Ray | Todd Coffey | | 423 | 435 | -12 |
| 2006-07-07 | vs CIN | 87 | L 5-10 | 38-49 | 4 | 32,315 | Horacio Ramirez | Eric Milton | Eric Milton | Horacio Ramirez | | 428 | 445 | -17 |
| 2006-07-08 | vs CIN | 88 | W 4-1 | 39-49 | 4 | 44,718 | John Smoltz | Aaron Harang | John Smoltz | Aaron Harang | Ken Ray | 432 | 446 | -14 |
| 2006-07-09 | vs CIN | 89 | W 8-3 | 40-49 | 3 | 31,908 | John Thomson | Bronson Arroyo | Oscar Villarreal | Bronson Arroyo | | 440 | 449 | -9 |
| 2006-07-14 | @ SDN | 90 | W 15-12 | 41-49 | 2 | 42,869 | Tim Hudson | Chris Young | Jorge Sosa | Clay Hensley | Tyler Yates | 455 | 461 | -6 |
| 2006-07-15 | @ SDN | 91 | W 11-3 | 42-49 | 2 | 39,988 | John Smoltz | Chan Ho Park | John Smoltz | Chan Ho Park | | 466 | 464 | 2 |
| 2006-07-16 | @ SDN | 92 | W 10-5 | 43-49 | 2 | 31,650 | Chuck James | Jake Peavy | Chuck James | Jake Peavy | | 476 | 469 | 7 |
| 2006-07-17 | @ SLN | 93 | W 15-3 | 44-49 | 2 | 44,507 | Horacio Ramirez | Jeff Weaver | Horacio Ramirez | Jeff Weaver | | 491 | 472 | 19 |
| 2006-07-18 | @ SLN | 94 | W 14-5 | 45-49 | 2 | 44,718 | Tim Hudson | Jason Marquis | Tim Hudson | Jason Marquis | | 505 | 477 | 28 |
| 2006-07-19 | @ SLN | 95 | L 3-8 | 45-50 | 2 | 43,991 | Jason Shiell | Chris Carpenter | Chris Carpenter | Jason Shiell | | 508 | 485 | 23 |
| 2006-07-21 | @ PHI | 96 | L 5-6 | 45-51 | 2 | 32,833 | John Smoltz | Cory Lidle | Cory Lidle | Ken Ray | Tom Gordon | 513 | 491 | 22 |
| 2006-07-23 | @ PHI | 97 | W 5-1 | 46-51 | 2 | 31,664 | Horacio Ramirez | Brett Myers | Macay McBride | Brett Myers | | 518 | 492 | 26 |
| 2006-07-24 | @ PHI | 98 | W 10-8 | 47-51 | 2 | 28,864 | Tim Hudson | Cole Hamels | Tim Hudson | Cole Hamels | Bob Wickman | 528 | 500 | 28 |
| 2006-07-25 | vs FLO | 99 | L 1-2 | 47-52 | 2 | 33,357 | Chuck James | Anibal Sanchez | Anibal Sanchez | Chuck James | Joe Borowski | 529 | 502 | 27 |
| 2006-07-26 | vs FLO | 100 | W 6-5 | 48-52 | 2 | 32,209 | John Smoltz | Josh Johnson | John Smoltz | Taylor Tankersley | Bob Wickman | 535 | 507 | 28 |
| 2006-07-27 | vs FLO | 101 | L 1-6 | 48-53 | 2 | 34,498 | Jason Shiell | Scott Olsen | Scott Olsen | Jason Shiell | | 536 | 513 | 23 |
| 2006-07-28 | vs NYN | 102 | L 4-6 | 48-54 | 3 | 53,943 | Horacio Ramirez | Pedro Martinez | Pedro Martinez | Horacio Ramirez | Billy Wagner | 540 | 519 | 21 |
| 2006-07-29 | vs NYN | 103 | L 3-11 | 48-55 | 3 | 49,047 | Tim Hudson | Orlando Hernandez | Orlando Hernandez | Tim Hudson | | 543 | 530 | 13 |
| 2006-07-30 | vs NYN | 104 | L 6-10 | 48-56 | 3 | 40,526 | Chuck James | Tom Glavine | Darren Oliver | Chuck James | Billy Wagner | 549 | 540 | 9 |
| 2006-08-01 | @ PIT | 105 | W 4-2 | 49-56 | 4 | 22,145 | John Smoltz | Ian Snell | John Smoltz | Ian Snell | Bob Wickman | 553 | 542 | 11 |
| 2006-08-02 | @ PIT | 106 | W 3-2 | 50-56 | 3 | 21,064 | Horacio Ramirez | Paul Maholm | Tyler Yates | Salomon Torres | Bob Wickman | 556 | 544 | 12 |
| 2006-08-03 | @ PIT | 107 | L 2-3 | 50-57 | 4 | 17,324 | Tim Hudson | Shawn Chacon | Shawn Chacon | Tim Hudson | Mike Gonzalez | 558 | 547 | 11 |
| 2006-08-04 | @ CIN | 108 | L 4-5 | 50-58 | 4 | 33,661 | Chuck James | Aaron Harang | Aaron Harang | Chuck James | Eddie Guardado | 562 | 552 | 10 |
| 2006-08-05 | @ CIN | 109 | L 6-8 | 50-59 | 4 | 33,170 | Jason Shiell | Bronson Arroyo | David Weathers | Tyler Yates | Bill Bray | 568 | 560 | 8 |
| 2006-08-06 | @ CIN | 110 | W 6-4 | 51-59 | 3 | 29,660 | John Smoltz | Kyle Lohse | Macay McBride | Gary Majewski | Bob Wickman | 574 | 564 | 10 |
| 2006-08-07 | vs PHI | 111 | L 6-9 | 51-60 | 3 | 26,177 | Horacio Ramirez | Brett Myers | Brett Myers | Horacio Ramirez | | 580 | 573 | 7 |
| 2006-08-08 | vs PHI | 112 | W 3-1 | 52-60 | 3 | 30,714 | Tim Hudson | Cole Hamels | Tim Hudson | Cole Hamels | Bob Wickman | 583 | 574 | 9 |
| 2006-08-09 | vs PHI | 113 | L 3-9 | 52-61 | 3 | 27,222 | Chuck James | Randy Wolf | Rick White | Tyler Yates | | 586 | 583 | 3 |
| 2006-08-11 | vs MIL | 114 | W 2-1 | 53-61 | 4 | 31,336 | John Smoltz | Chris Capuano | John Smoltz | Derrick Turnbow | | 588 | 584 | 4 |
| 2006-08-12 | vs MIL | 115 | L 5-8 | 53-62 | 4 | 40,480 | Kevin Barry | Ben Sheets | Ben Sheets | Kevin Barry | Francisco Cordero | 593 | 592 | 1 |
| 2006-08-13 | vs MIL | 116 | W 7-4 | 54-62 | 4 | 34,718 | Tim Hudson | Tomo Ohka | Chad Paronto | Matt Wise | Bob Wickman | 600 | 596 | 4 |
| 2006-08-14 | @ WAS | 117 | W 10-4 | 55-62 | 3 | 21,550 | Chuck James | Ramon Ortiz | Chuck James | Ramon Ortiz | | 610 | 600 | 10 |
| 2006-08-15 | @ WAS | 118 | L 0-5 | 55-63 | 3 | 24,036 | Lance Cormier | Pedro Astacio | Pedro Astacio | Lance Cormier | | 610 | 605 | 5 |
| 2006-08-16 | @ WAS | 119 | L 6-9 | 55-64 | 4 | 28,094 | John Smoltz | Billy Traber | Billy Traber | John Smoltz | Chad Cordero | 616 | 614 | 2 |
| 2006-08-17 | @ WAS | 120 | W 5-0 | 56-64 | 3 | 29,007 | Oscar Villarreal | Jason Bergmann | Oscar Villarreal | Jason Bergmann | | 621 | 614 | 7 |
| 2006-08-18 | @ FLO | 121 | W 6-1 | 57-64 | 3 | 19,161 | Tim Hudson | Scott Olsen | Tim Hudson | Scott Olsen | | 627 | 615 | 12 |
| 2006-08-19 | @ FLO | 122 | W 5-3 | 58-64 | 3 | 21,428 | Chuck James | Ricky Nolasco | Chuck James | Ricky Nolasco | Bob Wickman | 632 | 618 | 14 |
| 2006-08-20 | @ FLO | 123 | L 3-4 | 58-65 | 3 | 16,461 | Lance Cormier | Dontrelle Willis | Dontrelle Willis | Tyler Yates | Joe Borowski | 635 | 622 | 13 |
| 2006-08-21 | vs PIT | 124 | W 3-0 | 59-65 | 3 | 21,898 | John Smoltz | Zach Duke | John Smoltz | Zach Duke | Bob Wickman | 638 | 622 | 16 |
| 2006-08-22 | vs PIT | 125 | L 3-5 | 59-66 | 3 | 21,830 | Oscar Villarreal | Shawn Chacon | Damaso Marte | Danys Baez | Mike Gonzalez | 641 | 627 | 14 |
| 2006-08-23 | vs PIT | 126 | L 4-5 | 59-67 | 4 | 23,082 | Tim Hudson | Ian Snell | Matt Capps | Chad Paronto | Mike Gonzalez | 645 | 632 | 13 |
| 2006-08-25 | vs WAS | 127 | L 6-7 | 59-68 | 4 | 33,621 | Chuck James | Ramon Ortiz | Ryan Wagner | Chad Paronto | Saul Rivera | 651 | 639 | 12 |
| 2006-08-26 | vs WAS | 128 | W 10-1 | 60-68 | 4 | 38,610 | John Smoltz | Pedro Astacio | John Smoltz | Pedro Astacio | | 661 | 640 | 21 |
| 2006-08-27 | vs WAS | 129 | W 13-6 | 61-68 | 4 | 30,587 | Oscar Villarreal | Billy Traber | Macay McBride | Billy Traber | | 674 | 646 | 28 |
| 2006-08-29 | vs SFN | 130 | W 13-8 | 62-68 | 4 | 23,756 | Tim Hudson | Jason Schmidt | Tim Hudson | Jason Schmidt | | 687 | 654 | 33 |
| 2006-08-30 | vs SFN | 131 | W 5-3 | 63-68 | 4 | 24,952 | Chuck James | Brad Hennessey | Chuck James | Brad Hennessey | Bob Wickman | 692 | 657 | 35 |
| 2006-08-31 | vs SFN | 132 | L 6-8 | 63-69 | 4 | 24,748 | John Smoltz | Matt Morris | Matt Morris | John Smoltz | Armando Benitez | 698 | 665 | 33 |
| 2006-09-02 | @ PHI | 133 | W 4-3 | 64-70 | 4 | 31,717 | Oscar Villarreal | Jon Lieber | Tyler Yates | Arthur Rhodes | Bob Wickman | 702 | 668 | 34 |
| 2006-09-02 | @ PHI | 134 | L 4-16 | 64-70 | 4 | 28,600 | Kyle Davies | Scott Mathieson | Eude Brito | Kyle Davies | | 706 | 684 | 22 |
| 2006-09-03 | @ PHI | 135 | L 7-8 | 65-71 | 4 | 0 | Tim Hudson | Jamie Moyer | Geoff Geary | Bob Wickman | | 713 | 692 | 21 |
| 2006-09-03 | @ PHI | 136 | W 3-1 | 65-71 | 4 | 37,044 | Lance Cormier | Brett Myers | Chad Paronto | Geoff Geary | Bob Wickman | 716 | 693 | 23 |
| 2006-09-04 | @ NYN | 137 | W 5-0 | 66-71 | 4 | 42,428 | Chuck James | Steve Trachsel | Chuck James | Steve Trachsel | | 721 | 693 | 28 |
| 2006-09-06 | @ NYN | 138 | L 1-4 | 66-73 | 4 | 0 | John Smoltz | David Williams | David Williams | John Smoltz | Billy Wagner | 722 | 697 | 25 |
| 2006-09-06 | @ NYN | 139 | L 0-8 | 66-73 | 4 | 40,536 | Kyle Davies | Oliver Perez | Oliver Perez | Kyle Davies | | 722 | 705 | 17 |
| 2006-09-08 | vs CHN | 140 | W 8-4 | 67-73 | 4 | 30,977 | Tim Hudson | Angel Guzman | Tim Hudson | Angel Guzman | | 730 | 709 | 21 |
| 2006-09-09 | vs CHN | 141 | W 7-3 | 68-73 | 4 | 40,584 | Chuck James | Wade Miller | Chuck James | Wade Miller | | 737 | 712 | 25 |
| 2006-09-10 | vs CHN | 142 | W 2-1 | 69-73 | 4 | 28,212 | Lance Cormier | Juan Mateo | Lance Cormier | Juan Mateo | Bob Wickman | 739 | 713 | 26 |
| 2006-09-11 | vs CHN | 143 | L 3-8 | 69-74 | 4 | 19,444 | John Smoltz | Rich Hill | Rich Hill | John Smoltz | | 742 | 721 | 21 |
| 2006-09-13 | vs PHI | 144 | L 5-6 | 69-76 | 4 | 0 | Kyle Davies | Randy Wolf | Rick White | Chad Paronto | Tom Gordon | 747 | 727 | 20 |
| 2006-09-13 | vs PHI | 145 | L 2-7 | 69-76 | 4 | 22,233 | Tim Hudson | Jon Lieber | Jon Lieber | Tim Hudson | | 749 | 734 | 15 |
| 2006-09-14 | vs PHI | 146 | W 4-1 | 70-76 | 4 | 19,352 | Chuck James | Jamie Moyer | Chuck James | Jamie Moyer | Bob Wickman | 753 | 735 | 18 |
| 2006-09-15 | vs FLO | 147 | L 4-6 | 70-77 | 4 | 25,340 | Lance Cormier | Dontrelle Willis | Dontrelle Willis | Lance Cormier | Joe Borowski | 757 | 741 | 16 |
| 2006-09-16 | vs FLO | 148 | W 2-1 | 71-77 | 4 | 28,392 | John Smoltz | Anibal Sanchez | John Smoltz | Anibal Sanchez | Bob Wickman | 759 | 742 | 17 |
| 2006-09-17 | vs FLO | 149 | W 8-7 | 72-77 | 4 | 27,192 | Tim Hudson | Ricky Nolasco | Kevin Barry | Joe Borowski | | 767 | 749 | 18 |
| 2006-09-18 | @ WAS | 150 | W 6-1 | 73-77 | 4 | 25,211 | Kyle Davies | Tony Armas | Kyle Davies | Tony Armas | | 773 | 750 | 23 |
| 2006-09-19 | @ WAS | 151 | L 2-9 | 73-78 | 4 | 20,596 | Chuck James | Beltran Perez | Beltran Perez | Chuck James | | 775 | 759 | 16 |
| 2006-09-20 | @ WAS | 152 | W 7-3 | 74-78 | 4 | 19,027 | Lance Cormier | Ramon Ortiz | Lance Cormier | Ramon Ortiz | | 782 | 762 | 20 |
| 2006-09-21 | @ COL | 153 | W 6-3 | 75-78 | 4 | 18,499 | John Smoltz | Byung-Hyun Kim | John Smoltz | Byung-Hyun Kim | Bob Wickman | 788 | 765 | 23 |
| 2006-09-22 | @ COL | 154 | L 4-6 | 75-79 | 4 | 33,260 | Tim Hudson | Josh Fogg | Josh Fogg | Tim Hudson | Brian Fuentes | 792 | 771 | 21 |
| 2006-09-23 | @ COL | 155 | L 9-10 | 75-80 | 4 | 24,300 | Kyle Davies | Jeff Francis | Jeff Francis | Kyle Davies | Brian Fuentes | 801 | 781 | 20 |
| 2006-09-24 | @ COL | 156 | L 8-9 | 75-81 | 4 | 30,216 | Chuck James | Juan Morillo | Jeremy Affeldt | Tyler Yates | Brian Fuentes | 809 | 790 | 19 |
| 2006-09-26 | vs NYN | 157 | W 12-0 | 76-81 | 3 | 22,607 | John Smoltz | Oliver Perez | John Smoltz | Oliver Perez | | 821 | 790 | 31 |
| 2006-09-27 | vs NYN | 158 | W 13-1 | 77-81 | 3 | 23,177 | Tim Hudson | Pedro Martinez | Tim Hudson | Pedro Martinez | | 834 | 791 | 43 |
| 2006-09-28 | vs NYN | 159 | L 4-7 | 77-82 | 3 | 22,944 | Kyle Davies | Orlando Hernandez | Orlando Hernandez | Kyle Davies | | 838 | 798 | 40 |
| 2006-09-29 | vs HOU | 160 | W 4-1 | 78-82 | 3 | 31,034 | Chuck James | Roger Clemens | Chuck James | Roger Clemens | Bob Wickman | 842 | 799 | 43 |
| 2006-09-30 | vs HOU | 161 | L 4-5 | 78-83 | 3 | 40,123 | Lance Cormier | Andy Pettitte | Trever Miller | Bob Wickman | Dan Wheeler | 846 | 804 | 42 |
| 2006-10-01 | vs HOU | 162 | W 3-1 | 79-83 | 3 | 36,030 | John Smoltz | Chris Sampson | John Smoltz | Chris Sampson | Bob Wickman | 849 | 805 | 44 |