McGowan, whose slow recovery from surgery on his right shoulder has created concerns about his career, underwent an operation to repair cartilage on his left knee earlier this month. McGowan injured his knee during routine running drills and went under the knife on July 9.
Blue Jays general manager J.P. Ricciardi said McGowan needed six weeks to make his way back from the knee surgery, bringing to a halt the pitcher's throwing program. The bigger concern continues to be McGowan's gradual comeback from the shoulder procedure he underwent on July 31 of last season.
"His knee's probably going to be fine," Blue Jays manager Cito Gaston said. "I think the main thing is we're worried about his shoulder. He's a nice young man. I'd like to see him back with a good arm. I just worry about his future -- not so much about getting him back."
Ricciardi said that the 27-year-old McGowan, who was projected to be the club's No. 2 starter this season before injuring his arm a year ago, did not seem like a candidate to take part in winter ball after this season. The Blue Jays hope McGowan can be a factor in 2010, but will wait to see how the right-hander looks during Spring Training.
"I feel bad for the poor kid," Ricciardi said.
McGowan emerged as one of the most promising young arms on the Blue Jays' starting staff in 2007, when he went 12-10 with a 4.08 ERA over 27 outings. Last year, McGowan went 6-7 with a 4.37 ERA before being sidelined with the shoulder issue. Toronto selected McGowan in the first round (33rd overall) in the 2000 First-Year Player Draft.
Following McGowan's shoulder surgery last season, the Blue Jays initially hoped he might be ready to rejoin the rotation in May of this year. During the spring, it quickly became clear that McGowan was not going to be ready by then.
In May, when Toronto took part in an Interleague road series against Atlanta, McGowan began to work through a long-toss program and hoped to be back on a mound in June. McGowan expressed optimism about possibly being ready to return to the Jays before the end of this season.
Gaston said the Blue Jays weren't as confident that McGowan would return this year.
"Not really," Gaston said. "He's just somebody that you put on the back burner. I think about him for his sake and hope that he can come back and pitch again for himself. But I don't certainly think about him as coming back pitching any time soon."
Jordan Bastian is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.