Report: 49ers QB Colin Kaepernick has surgery on thumb, also knee

SANTA CLARA, Calif. -- Not only did San Francisco 49ers quarterback Colin Kaepernick undergo surgery on his injured right thumb Wednesday in Vail, Colorado, according to reports, he also had a procedure done on his left knee, the Sacramento Bee reported.

The 49ers would not confirm the procedures.

Kaepernick was in Colorado for a check-up on his surgically repaired left shoulder.

Since the start of the 2015 season, Kaepernick has had half as many surgeries, three, as touchdown passes, six.

It raises the question of whether Kaepernick will be healthy enough to pass a physical on April 1, when $11.9 million of his contract for the 2016 season becomes fully guaranteed.

"Once again, I'm preparing to be healthy and win the Super Bowl," Kaepernick said in the 49ers' locker room on Monday. "That's all my focus is."

Kaepernick injured the thumb in the Niners' 20-3 loss to the Seattle Seahawks on Oct. 22, and he injured the knee a week later in a 27-6 loss at the St. Louis Rams, according to the Bee. He was then benched in favor of Blaine Gabbert after being sacked 28 times in eight starts amid a 2-6 record.

Kaepernick was placed on season-ending injured reserve on Nov. 21 and underwent surgery to repair the torn labrum in his non-throwing shoulder.

He never appeared on the Niners' injury report for the shoulder or knee injuries, though he did for the hand injury after the Seahawks game; he showed up to the postgame news conference with the hand heavily bandaged.

Kaepernick said increased pain and swelling in the right thumb area made him decide to get an MRI last week, which revealed a torn ligament.

He got a second opinion during a Tuesday visit to the Steadman Clinic in Vail and underwent the recommended surgery Wednesday, according to multiple reports.

Niners general manager Trent Baalke was asked Monday why the thumb injury was not addressed during the season.

"I can't answer that," he said. "I think there's a process that these players go through. That would be a better question answered by our medical staff."

With the 49ers undergoing a coaching search for the second time in 12 months, the new coach will have input on who the quarterback is next season, Baalke said.

Niners CEO Jed York said, "I love Colin. He's been a great piece of this team for a long time. He has certainly helped us get to the level of success that we've had.

"Right now, I want to make sure that Colin gets back healthy. ... I want to make sure that he continues to improve."