The 49ers issued a statement Friday that they knew of the injury to the former University of Nevada quarterback before they selected him with the No. 36 pick in April'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 the quarterback would have avoided surgery if not for the NFL lockout.
"That was part of the decision -- should he take care of it? Should he wait?" Smith told The Sacramento Bee. "He certainly could have (waited). He played four games at Nevada [with the injury] and barely talked about it. Because of the lockout, the timing was as good as it's going to get."
Smith said teams were aware of the issue prior to the draft.
Kaepernick, who did not disclose the nature of his injury, 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.
"For me, going through the end of the season and then on to the Senior Bowl and everything, there wasn't any time to get it handled ...," Kaepernick told The Bee.
The 49ers have big expectations for their new quarterback.
Kaepernick, the only player in NCAA history to rush for more than 4,000 career yards while throwing for more than 10,000, amassed 3,022 passing yards and ran for another 1,206 for the Wolfpack last season -- he had 59 rushing touchdowns in 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- (No. 45 overall), fourth- (No. 108) and fifth-round (No. 141) 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 to show he can be the longtime solution at quarterback.
Although 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.
"I don't feel like (the surgery is) going to slow me down at all," Kaepernick said. "I'll be ready for the season, ready for training camp. I'll be ready."
The Associated Press contributed to this report.