Dr. James Andrews performed the procedure on the Cubs pitcher in Birmingham, Ala. During the arthroscopy, Andrews did a debridement of Prior's right rotator cuff, as well as repair the labral and capsular injuries in his right shoulder.
"It's not career-ending," Hendry said Wednesday. "[Andrews] felt optimistic that he would be able to pitch next year. A couple hours after surgery, [Andrews] wasn't going to give you a time frame. He didn't think there was anything significant to stop Mark from pursuing his career, and at his age, should not have a problem responding and coming back after probably a strenuous rehab."
The Cubs announced in a statement that Prior will not pitch this year, and will continue his rehab program this offseason. He got started on Wednesday in Birmingham, and the program will be overseen by Andrews and the Cubs' medical staff.
"Obviously, he had some things wrong physically and he's getting them corrected," Cubs manager Lou Piniella said. "This is a step in the right direction."
Prior, 26, has been on the disabled list at least once every year since he was called up in May 2002, but had never had surgery on his shoulder until now.
The right-hander pitched 10 1/3 innings this spring with the Cubs, and looked sharp at times, but his control and velocity was off, and he rarely hit 87 mph. He never reported any pain or problems with his shoulder in Spring Training, which was encouraging, and said he felt ready to pitch this season.
"There were no complaints in Spring Training at all about discomfort or sharp pain," Hendry said. "He wouldn't have been pitching the last couple times out if he had [problems]."
Wade Miller won the fifth-starter spot for the Cubs and the team optioned Prior to Triple-A Iowa. However, Prior never reported to the Minor League team and was placed on the disabled list with right shoulder fatigue.
Prior rehabbed at the Cubs' extended Spring Training camp in Mesa, Ariz., and his only outing there was two innings on April 12, but that was cut short because of discomfort in his shoulder. Since then, he was examined by orthopedic specialists Lewis Yocum and Andrews.
"I think we all felt it was time to have Dr. Andrews go in and scope and look around and fix up some things," Hendry said. "When you pitch in the Major Leagues, any time you go in and scope somebody's shoulder, you can find some things to touch up."
Prior was limited to nine starts in 2006 because of his shoulder. He hasn't been the same since a stellar 2003 season when he won 18 games and was named to the All-Star team.
"Obviously, when you have discomfort on and off in a continued fashion over a long period of time, you have to assume something is causing the discomfort," Hendry said. "There's no reason to ever think he didn't want to pitch. He was certainly disappointed when he didn't make the ballclub this year."
Hendry had not talked to Prior since the procedure, but talked to Cubs athletic trainer Mark O'Neal and Prior's agent, John Boggs. They were encouraged that Prior did not require anything more than arthroscopic surgery.
"He's 26 years old and obviously has a lot of years to get it right," Hendry said.
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.