The 2005 Cy Young Award winner, who hasn't pitched since Opening Night, is expected to be sidelined for at least three more months. Dr. George Paletta, the Cardinals' head team physician, will perform the operation on Tuesday.
"That's a huge hit," said manager Tony La Russa. "But that's part of the game, part of baseball. Our goal now is to be in contention when he gets back."
Carpenter won't throw a ball for roughly six weeks after the surgery. From there, it will likely be at least six weeks before he is able to pitch competitively in a game. It is hoped and expected, but not guaranteed, that he will be able to return to active duty before the season ends.
"We need to get it taken care of so the rest of the season's not in jeopardy also," Carpenter said. "Hopefully, we can go in and get it done and my recovery will be faster than everybody hopes."
The right-hander came down with inflammation and swelling in his elbow following his start in the season opener against the Mets on April 1. It was determined that the discomfort was caused by bone spurs, and that Carpenter also had some arthritis in the elbow.
Paletta emphasized that the spurs are the major problem. They cause impingement when Carpenter's elbow reaches full extension, such as at the release point when he throws.
"We had hoped not to get to this point, but as we thought it was a possibility, we've reached a point where I think there is no option except to go ahead surgically and scope the elbow and clean the elbow out," Paletta said.
When the problem first arose, Carpenter rested for a few days, then threw a side session in Houston the following weekend. Though he felt fine while throwing, the swelling and stiffness returned the following day.
The club and Carpenter opted against surgery at that point, attempting to combat the condition with aggressive treatment and rest. Carpenter took two weeks off without throwing a ball before beginning a new throwing program.
Carpenter threw a bullpen session on April 28, and he reported no problems the following day -- a very encouraging development. On Tuesday in Milwaukee, he threw three simulated innings. But he began to feel some discomfort after that throw, and when it didn't subside, the path became clear.
"It was pretty sore the next day after I threw," Carpenter said. "I was hoping it was just from not throwing with that intensity for a while. But, unfortunately, Thursday was just as bad. We tried to do everything we could to see if we could get through it, and it wasn't going to happen."
Paletta examined Carpenter on Saturday, after which the team announced that the pitcher will have the operation. Carpenter has had surgery to remove spurs before. Paletta specified that the condition is accurately considered spurs, rather than chips, which are free-floating bodies in the elbow.
"I was happy with the way it went when I threw my bullpen, and I was happy with the way it went when I threw my simulated game," Carpenter said. "Unfortunately, again, the results afterwards weren't what we were looking for. It got to the point where it's either do it or continue to battle this."
Brad Thompson will start for the Cardinals on Tuesday. How long he remains in the rotation is an open question, but he will at least get the chance to prove himself.
"We're going to give Brad an opportunity if he pitches well enough to deserve it," said pitching coach Dave Duncan. "I'm open-minded about it."
Thompson, who last pitched on May 1, threw a bullpen session before Saturday's game. That would put him on schedule for the next open spot in the St. Louis rotation, on Tuesday against the Rockies at Busch Stadium.
Matthew Leach is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.