Late Wednesday, the Cubs opted to not tender a contract to Prior, who missed all of last season. He underwent arthroscopic surgery on his right shoulder in April, and it was uncertain when he would be able to return.
"Obviously, we all wish Mark had stayed healthy and continued on the tremendous track he was on for a few years," Cubs general manager Jim Hendry said. "At the end of the day, the rules of the game prohibit you from having the decisions you'd like to make sometimes. Mark is in his free agent year.
"It really wasn't a difficult decision, as it was an unfortunate decision," Hendry said.
Prior, an 18-game winner and All-Star in 2003, made $3.575 million in 2007, and was arbitration eligible. He will be a free agent after the 2008 season.
"I felt, in the best interest of the Chicago Cubs, that the only way it would've been workable for us is if Mark or John Boggs, his representative, would've been agreeable to a lesser number on the base in 2008 and my request mainly would've centered on having a club option for 2009," Hendry said. "That was the comfort zone we had with him. That doesn't mean the player has to accept that or the agent. In their case, that wasn't received real well.
"There weren't any hard feelings, there wasn't any animosity," Hendry said. "That's what negotiated rights are for -- arbitration, free agent process. That's the path John Boggs and Mark chose to take."
One of the problems is that no one could predict when Prior would be able to pitch in 2008, and Hendry said the Cubs medical staff felt the right-hander would not be completely ready until 2009.
Prior, 27, is now a free agent and able to negotiate with all 30 teams. That includes the Cubs.
"I would never rule out someone like Mark returning here, whether it's someday sooner or someday later," said Hendry, who added that Boggs said they wouldn't close the door on the Cubs.
Prior was 42-29 with a 3.51 ERA in 106 starts for the Cubs since he made his big league debut in 2002. He's been on the disabled list every season, but some of his injuries have been because of freak accidents. He collided with Marcus Giles while running the bases in 2003, and he fractured a bone in his right elbow when he was hit by a line drive in 2005.
In his first season with the Cubs, Cotts, 27, split time between the Cubs and Triple-A Iowa. He was on the big league team's Opening Day roster, and went 0-1 with a 4.86 ERA in 16 relief appearances before being optioned to Iowa on May 20, where he spent the remainder of the season. The lefty posted a 2-2 record with a 4.83 ERA in 24 appearances, including six starts.
"We never gave up on Neal Cotts," Hendry said. "It wasn't a matter of his arm strength. He's a very competitive and caring guy as far as wanting to do well. He was probably a victim of his own trying too hard to make it work."
Hendry said Cotts threw well the last few weeks at Iowa.
"In hindsight, I should've brought him up in September," Hendry said.
Instead, the Cubs relied on lefties Scott Eyre, Will Ohman and Carmen Pignatiello.
"Neal threw well enough to get himself in the mix to come to camp and try to win a job in '08," 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.