MINNEAPOLIS (AP) — Scott Baker has struggled with pain in his pitching elbow for more than a year now, and the right-hander finally will have surgery to fix the problem once and for all. The injury, and the surgery, couldn't have come at a worse time for Baker or the Minnesota Twins.

Baker will have surgery to repair the flexor pronator tendon in his right elbow, the team announced on Wednesday. He will miss the entire season while rehabbing, which puts the Twins rotation in a serious bind and throws his pitching future into flux. Baker will be a free agent after this season, and the injury could severely impact the 30-year-old's value on the open market.

The tendon has bothered Baker for the last couple of seasons and he says he can no longer pitch through the pain. He got a second opinion this week and was told he needed surgery, which requires six months of rehab.

"It's been a battle and unfortunately it's a losing battle at this point," Baker said before the winless Twins took on the Los Angeles Angels. "The training staff and I have done everything we possibly could to pitch through it."

Baker hit the disabled list twice last season with discomfort in his elbow, derailing the best season on the staff last year. He started on opening day and went 8-6 with 3.14 ERA in 21 starts. He said the pain went away in the offseason, but flared up again once he started ramping up his workouts in spring training to get ready for 2012.

The Twins' medical staff and Baker tried to devise a program that would allow him to pitch through the pain, but it didn't work out.

"We never got him right this spring," general manager Terry Ryan said. "We thought things were progressing, and it came down to either he can pitch with this or he can't. He can't. So he's going to get it repaired."

If there is any good news, it's that he does not need Tommy John surgery, the elbow ligament replacement procedure that often requires more than a year of recovery time. Baker initially was diagnosed with an elbow strain, but sought a second opinion from Dr. David Altcheck in New York this week. Altcheck told Baker that he needed surgery, but that his ulnar collateral ligament appeared to be in fine shape.