If there is a positive, it's that Lilly will have an arthroscopic procedure done on Monday on his left knee while he's sidelined, which will allow him to rehab both his shoulder and knee at the same time.
"What we need to do is keep hanging in there," Cubs manager Lou Piniella said.
The Cubs were one of two Major League teams to begin the season without a player on the disabled list, but since May 4, they have had 13 players go on the DL 14 times. Pitcher Ryan Dempster (broken right toe) is expected to be activated on Tuesday.
The Cubs recalled pitcher Justin Berg from Triple-A Iowa to take Lilly's spot on the roster, but Berg will go into the bullpen, not the rotation. The right-hander, a native of Antigo, Wis., was 4-1 with a 2.00 ERA in 24 relief appearances, and has given up one home run in 36 innings, and that was in his third outing of the year.
Lilly said he does not feel that his sore knee, which has bothered him since early June, was the reason for his shoulder problems.
"I would be really surprised if they put that together," he said. "I don't think so, because with the exception of the last start in Philly, I was pitching pretty good. I didn't feel I was compromising my delivery because of my knee."
Against the Phillies on Monday, Lilly served up a career-high nine runs on eight hits over four innings, striking out six.
"[My shoulder] got my attention the day after in Philly," he said. "There are times during the season you feel something, and you keep going and it goes away and it's nothing that's alarming. The day after in Philly, it felt a little unusual. The more I tried to throw, the worse it got. [On Friday], I went out to try to throw and there was a sharp pain in front of my shoulder that I hadn't experienced before."
Lilly underwent an arthrogram on Friday, which confirmed the inflammation. Lilly said he had a similar problem in 2005 when he was with Toronto, and he recognized the symptoms.
"The first time in Toronto that I went on the DL, it was an AC joint," Lilly said. "The second time, it was the same symptoms. I tried to pitch with it for a few innings and I couldn't pitch effectively. I don't think I was throwing over 80 miles an hour."
Lilly felt he could continue to pitch despite his sore knee. But the shoulder is a different story.
"When I come back, I want to be healthy, and I want to be prepared to win and be effective," he said. "I don't know how long that will take. I want to get on the field as soon as I can."
The Cubs began Saturday 1 1/2 games back in the National League Central, and Lilly said it will be difficult to be sidelined now.
"One of the most frustrating things is we're right there and we have a chance to move into the lead in this division," Lilly said. "The frustrating part is knowing I'd like to be a part of that and help us do that, but, unfortunately, I'm going to have to watch for a little while."
Chicago's rotation now will feature Dempster, Carlos Zambrano, Rich Harden and rookies Randy Wells and Kevin Hart. The Cubs did consider moving Sean Marshall from the bullpen to the rotation, but Marshall is the only lefty reliever. They also discussed possibly starting Jeff Samardzija.
"The problem is if we get short starts from either [Hart or Harden], our bullpen will really be taxed for the Houston series," Piniella said of the upcoming four-game series against the Astros that starts Monday.
Does this change the Cubs' approach with Friday's non-waiver Trade Deadline coming up?
"I don't think that Jim [Hendry, general manager] will go in that direction," Piniella said. "I think we'll go with what we have and hang in there and get healthy and make a run. We're in good position. We just have to maintain our position and continue to win some baseball games.
"These kids are capable of pitching the same way a veteran is. Wells has done a nice job and hopefully Hart can hold his own until we get Lilly back."