NEW YORK – Two MRI exams failed to detect a torn ligament in Scott Baker’s right elbow, but when an orthopedic surgeon opened it up Tuesday, April 17, there was no question:

The Twins starter needed Tommy John surgery.

Baker had surgery to repair the unlar collateral ligament in his elbow Tuesday, another piece of bad news in a 2012 season that so far has failed to meet even the most conservative expectations.

“It wasn’t a shock,” general manager Terry Ryan said. “It’s not the scenario that anyone was hoping for, I know that, but they did prep Scott for that (possibility).”

Baker, 30, was scheduled for surgery to clean scar tissue off a flexor tendon, a procedure that would have required about six months of rehabilitation. Instead, he will miss at least 12 months. Named for the pitcher who first underwent the procedure, Tommy John surgery uses a ligament or tendon from another part of the patient’s body to repair or replace the damaged elbow ligament, in this case the one on the inside of the arm.

In Baker’s case, the ligament was repaired, not replaced.

Though two MRI exams failed to detect a tear, orthopedic specialist David Altchek believed full surgery was necessary in case a tear was detected in the operating room, Ryan said.

“That’s why they didn’t scope it. They wanted to go in and make sure that if that ligament had to be repaired, they’d do it in this surgery,” the GM said. “When you look at a picture, an MRI, it didn’t look like they needed to. But, (Baker) was guarded, I can tell you that.”

Baker never pitched this season, staying behind in spring training to work through forearm and elbow tenderness, which twice put him on the disabled list in 2011. After his first spring training start, he expressed optimism and spoke of being proactive about staying healthy with new exercises. But as spring progressed, it became clear something was still bothering him.

In his last start, with Class A Fort Myers on April 5, Baker threw 11 pitches before leaving the game. Baker was not available for comment Tuesday.

He sat with Ryan at Target Field on April 11 and announced his intention to have season-ending surgery to fix his tendon, and expressed confidence that his UCL was healthy.

“Obviously, the tendon is not very good, but the ligament is,” he said. “So in my case, (Dr. Altchek) didn’t express concern for the ligament.”

There must have been some, though, because before Tuesday’s surgery, Baker gave Altchek permission to repair the ligament if there was any damage.

“They did prep Scott for that. Scotty told me that,” Ryan said. “So unfortunately they had to repair it. The ligament did not look good to the doctor, so they did the UCL.”

Baker is in the final season of a four-year, $15.25 million extension paying him $6.5 million in 2012. Tommy John surgery has a high success rate among pitchers – Twins Carl Pavano and Francisco Liriano are among many who have returned from it – but recovery time is typically between 12 to 16 months, making it highly unlikely the Twins will pick up their $9.25 million option on Baker for 2013.

If they don’t, Baker will become an unrestricted free agent after the season.