Orthopedic surgeon Dr. Lewis Yocum performed the surgery in Los Angeles. He found no major damage to Lilly's shoulder, and the one-hour procedure consisted of a washout and clean up of the shoulder.
"All the news that I've been given leads me to believe it was the right decision," Lilly said Wednesday. "It was something I didn't want to do, but I also started to feel that after a month and it still wasn't getting better, I had thoughts of going into the  season trying to battle through shoulder problems all year and I didn't want to do that. I thought if I get it taken care of now and get it behind me, I'd be all right."
Lilly said he would've had the procedure done sooner in the offseason if he had known his shoulder wasn't going to bounce back.
"From Ted's point of view, it will give him comfort that there is no significant damage," Cubs general manager Jim Hendry said. "Now he goes about his business with an outstanding rehab and he can possibly be stronger than he was in . He's still got some career after ."
Lilly will immediately begin an aggressive range of motion and strengthening program. He'll be re-examined around Jan. 1, when a throwing program will be put in place. Typically, recovery time for a procedure such as this would place Lilly's return to the Cubs rotation sometime in April.
Hendry said Lilly's situation doesn't mean the Cubs now will be looking for a starting pitcher this offseason. Hendry and his staff were meeting this week with members of the Ricketts family, who took over ownership of the Cubs last week, during the organizational meetings in Arizona.
Among the topics to be discussed are what to do with potential free agents Rich Harden, John Grabow, Reed Johnson and Kevin Gregg. A player must file within 15 days after the World Series is over. The Cubs will retain exclusive negotiating rights during that 15-day period. Hendry has had discussions with agents representing all of the players.
Lilly, 33, was 12-9 with a 3.10 ERA this past season, recording a career-high 21 quality starts. He is coming off his fourth straight season with at least 150 strikeouts. The Cubs' only All-Star in 2009, Lilly was on the disabled list in July because of inflammation in his left shoulder.
"At the conclusion of the 2009 season, Cubs team doctors prescribed a conservative approach to managing Ted's shoulder in preparation for the 2010 season and, following a second opinion, Dr. Yocum agreed," Hendry said. "At the end of last week, Ted decided that undergoing a surgical procedure was the course of action he wanted to pursue, a decision the club supported. We're glad the surgery did not reveal any major damage to Ted's shoulder and look forward to his return to our rotation."
Lilly wanted to go into 2010 with a clean bill of health.
"I just didn't want to go into the season kind of doing what I was doing at the end of the year where I was missing starts and that sort of thing," Lilly said. "My symptoms were affecting the way I was throwing. I didn't feel I was able to throw the ball, [No. 1] without pain, and [No. 2] from the normal arm slot that I need to.
"All in all, the news is good," Lilly said. "There wasn't anything either structurally wrong with my shoulder or any significant damage. All the feedback that I get from Dr. Yocum and our training staff and everything is that we have expectations of getting back pretty soon from this."
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.