Lilly is coming back from arthroscopic surgery on his left shoulder and was slowed this spring when he was sidelined with the flu. He was then stalled because of back stiffness, which flared up last Friday.
On Wednesday night, he served up a solo homer to Memphis' Tyler Greene in the first. In his outing, Lilly walked one and struck out four. He was pulled after throwing 51 pitches, 31 for strikes.
"It was fun just being back on the mound," Lilly told reporters in Des Moines. "Everything went well. I'm pretty sure I'll feel good when I wake up."
The Iowa Cubs won, 5-2. Lilly gave way to Jay Jackson, who was the initial scheduled starter, and Jackson gave up two hits over five innings.
Lilly was expected to make one more Minor League start and if all goes well, he could start either in Milwaukee April 23-25, or during the Cubs' next homestand when they entertain the Nationals April 26-28.
"We had talked about the last week of April being the timetable for him, and if everything goes right, that's exactly when it'll be," Cubs manager Lou Piniella said.
Speaking of the rotation, the Cubs have tweaked theirs for the upcoming series vs. the Astros, and it'll be Carlos Silva on Friday, Tom Gorzelanny on Saturday, and Ryan Dempster on Sunday.
When Lilly does return, the Cubs will have to tweak their rotation and someone will go to the bullpen.
"We'll let everybody pitch until that happens," Cubs general manager Jim Hendry said. "It'll be a good problem to have if everybody is pitching good."