School officials say the concern is their nutritional value, or lack thereof. Each bag of Flamin' Hot Cheetos contains 26 grams of fat and a quarter of the amount of salt that's recommended for the entire day.
One school district in Illinois, which used to sell about 150,000 bags each year, has already taken the snack off its menu.
"If children were to bring in snacks that are high in fat, high in calories, that's their choice," Rockford School District Interim Superintendent Robert Willis said. "We're not going to be providing those kinds of foods."
On top of the artificial coloring and flavoring, some experts say the Cheetos are "hyperpalatable," meaning they're highly addictive.
"Our brain is really hardwired to find things like fat and salt really rewarding and now we have foods that have them in such high levels that it can trigger an addictive process," said Ashley Gearhardt, a clinical psychologist at the University of Michigan.
Frito Lay, which makes and sells Cheetos, says it is "committed to responsible and ethical practices, which includes not marketing our products to children ages 12 and under."
While Flamin' Hot Cheetos are under fire in schools, kids can't get enough of them. So much so that there is a YouTube video featuring kids rapping about their love of the snack.
"Got my fingers stained red and I can't get them off me. You can catch me and my crew eating hot Cheetos and takis," one boy raps in the video.
Takis are a chili pepper- and lime-flavored corn snack.
The video has already been viewed more than 3.3 million times and there are even Facebook fan pages dedicated to the snack.
One fan page has more than 49,000 "likes," with many fans posting photos and videos with the snack.
"Don't feel like leaving to get food," one person writes. "So I'm eating Flamin' Hot Cheetos."