MINNEAPOLIS -- The Twins' rotation was dealt a huge blow on Wednesday, when general manager Terry Ryan announced that right-hander Scott Baker will undergo surgery to repair the flexor pronator tendon in his right elbow and will miss the remainder of the season.

Baker flew to New York this week to meet with Dr. David Altchek, who recommended the surgery, which will also repair scar tissue around his elbow. The recovery time is six months.

"We're going to get this done sooner rather than later," Ryan said during a news conference at Target Field. "He's going to get it done by Dr. Altchek out in New York. This isn't exactly the news that any of us wanted to hear. Scotty doesn't, I don't, the club doesn't, but this is where it is going to go. We're going to get it taken care of, then [he is] going to do the therapy and the rehab under our guidance, and hopefully, he'll be ready to go for the 2013 season."

Baker, who started the year on the disabled list with tendinitis in his elbow, underwent an MRI in Fort Myers, Fla., on Friday after leaving a rehab start with Class A Fort Myers after just 11 pitches.

The results of that exam were similar to those of an MRI performed in July, when he missed 18 games with a strained flexor pronator tendon. But he pitched well when healthy last season, posting a 3.14 ERA in 134 2/3 innings.

After Friday's MRI, Baker went to Altchek for a second opinion and was told he needed surgery.

"He said this is something that's not going to repair itself," Baker said. "It's not going to cure itself. It's something that needs to be taken care of. Fortunately, he said the [ulnar collateral] ligament looked great, so I guess in a way, as bad as this is, the flexor pronator tendon is what needs to be repaired. Nobody hates this more than me. So it's tough."

Baker struggled with his velocity this spring, and said that it was tough to get loose before his outings. He only threw 4 2/3 innings in Grapefruit League play, with his last outing coming on March 26, when he allowed seven runs over just 2 2/3 innings against the Rays.

"It's something that I've been battling for a while," Baker said. "I don't mind pitching through pain, as long as you don't have the chance to further the injury. But when it comes to a point where your velocity's not there and you don't have the ability to finish pitches like you know you're capable of doing, then something's got to be done."

Baker also could be done with the Twins, as the club holds a $9 million option for him for next year. He was drafted by the Twins in 2003 and has pitched with them since '05. He has a career 4.15 ERA with 770 strikeouts and 224 walks in 958 innings.

"Honestly, I can't think about that right now," he said. "The Twins are all I've known, and obviously, I enjoy it here, so I hope that's not the case."

The Twins are expected to replace Baker with in-house options this season, as Jason Marquis is close to returning after a stint with Double-A New Britain to start the year. The Twins will also give looks to right-handers Anthony Swarzak and Liam Hendriks. Swarzak made his first start of the year on Sunday, when Hendriks was out with food poisoning.

"You're going to find a spot for Marquis, and Swarzak threw the ball well, and [Hendriks] was one of our better performers in Spring Training," Ryan said. "We've got something to work with there. Our big issue has not been pitching. We haven't hit too much. Our pitchers have done a relatively decent job here. So let's give these guys a chance to settle in and see exactly what we've got in the rotation."