The 49ers issued a statement Friday that they knew of the injury to the former Nevada quarterback before they selected him with the 36th overall pick in last month's NFL draft.
"The 49ers are aware that Colin Kaepernick underwent a procedure to address a pre-existing injury and were fully aware of the injury at the time of the draft," the team said. "The 49ers have no concerns regarding his health and are confident that he will be ready for the 2011 NFL season."
The injury does not appear to be serious.
Kaepernick's agent, Scott Smith, said the procedure was performed at Stanford Hospital and considered minor. He said the injury began bothering Kaepernick at the end of last season, and he would've avoided surgery if not for the NFL lockout.
Kaepernick also participated at the Senior Bowl and the NFL combine. With the ongoing labor dispute essentially eliminating most offseason workouts, Kaepernick decided to have the surgery as a precaution.
"He'll be ready to go come training camp," Smith said.
The surgery was first reported by The Sacramento Bee. Kaepernick did not immediately respond to a phone call or text message from The Associated Press seeking comment.
The 49ers have big expectations for their new quarterback.
Kaepernick threw for 3,022 yards and ran for another 1,206 for the Wolfpack last season -- finishing with 59 rushing touchdowns over four years -- and his combination of arm strength and running ability make him an intriguing prospect under new coach Jim Harbaugh's West Coast offense.
The 49ers traded up in the second round of the draft to select Kaepernick, giving Denver their second-round (45th overall), fourth-round (108th) and fifth-round (141st) picks. Alex Smith is expected to return to San Francisco and be the presumed favorite to start next season, although the 2005 No. 1 overall pick hasn't been consistent enough yet to show he can be the longtime solution at quarterback.
While Harbaugh has said there will be a wide-open quarterback competition whenever football resumes, Smith's return could allow Kaepernick the time needed to develop into an NFL quarterback.
Training camp typically begins in early August. But the NFL lockout has dragged on and could push back training camp and even threaten the season.