Mold can develop in the white valve inside the cup when it remains wet or moist and not cleaned frequently, the agency said.
"The CPSC advises that mold ingestion poses a risk of gastrointestinal symptoms and infections in consumers with compromised immune systems," it said.
The sippy cup manufacturer, Mayborn USA, received 3,066 reports of mold in the removable one-piece valve — including 68 reports of children experiencing diarrhea, vomiting or other symptoms associated with drinking from the moldy valve, said the commission.
"Child health and wellbeing is at the heart of everything we do," said the company in a statement on Facebook. "We know that some people are continuing to experience difficulty in cleaning the white, one-piece valve in some of our sippy cups. For this, we sincerely apologise."
The recall follows several online complaints from parents who discovered mold building inside the valve.
After BuzzFeed reported on the complaints in February, the company said it was manufacturing "transparent, see-through valves immediately available to any parents that have concerns."
The transparent material would help parents see inside "and give them confidence that the valve is clean."
The recall affects Mayborn USA's First Sips Transition cup, Trainer Sippee cup, Sippee cup (including Cute Quips), Sportee bottle and Insulated Swiggle/Sippee tumblers.
The plastic cups have spill-proof tops, detachable handles and were sold with colored lids in a number of colors and prints.
Consumers are advised to immediately stop using the recalled Sippee cups and contact Mayborn to receive a free replacement cup, according to the Consumer Products Safety Commission.
The cups were sold at CVS, Giant, Kohl's, Marshalls, Sam's Club, Ross Stores, Target, Walgreens and Wal-Mart.