Boston College says several of its students, including members of the men's basketball team, complained of gastrointestinal symptoms after eating at a Chipotle restaurant in Boston.
The news sent the restaurant's shares broadly lower on Monday, as investors feared an outbreak that originated in other states could take a toll on Chipotle's sales.
The college, in a statement, said it had notified the state Department of Public Health, which is trying to determine if it is part of an ongoing national outbreak of e-coli that has been linked to the Chipotle chain.
A spokesman for the state agency said it appeared that more than 20 students were sickened, but it had not yet determined the cause of the illnesses.
In a statement, Chipotle said that "the safety and well being of our customers is always our highest priority, so our restaurant at Cleveland Circle in Boston is temporarily closed while we work with local health officials to investigate a number of illnesses among Boston College students."
It added: "We do not have any evidence to suggest that this incident is related the previous E. coli incident. There are no confirmed cases of E. coli connected to Chipotle in Massachusetts."
Meanwhile, the company's stock fell in after hours trading, as the company faces its first decline in a key sales figure after an outbreak of E. coli linked to its restaurants.
The chain known for touting its quality ingredients said Friday it expects sales to drop between 8 percent and 11 percent at established locations for the fourth quarter if current trends continue. That would mark the first time the figure fell since Chipotle went public in 2006.
Chipotle's stock ended the session off nearly 2 percent, at $551.75, on Monday. In extended trading, the stock swooned by more than 4 percent.
In a filing with the Securities and Exchange Commission, Chipotle said sales have been "extremely volatile" since it closed restaurants in Oregon and Washington in early November as a result of the outbreak. Sales plummeted by as much as 22 percent as additional cases were reported, and were down 16 percent for November.
The Centers for Disease Control and Prevention had said earlier Friday that the outbreak had widened and sickened 52 people in nine states. It has not yet identified the ingredient that made people sick.
The first cases were reported at the end of October, and the agency said the most recent illness started on Nov. 13
About 48 million people get sick from a foodborne illness each year, according to the CDC.
Chipotle Mexican Grill, based in Denver, says whatever the likely ingredient was that made people sick is out of its restaurants and that it is adopting stricter food safety standards.
The company, which has benefited from marketing its use of local ingredients, said some of its local produce suppliers might not be able to meet the new standards. Locally sourced produce accounts for a "relatively small percentage" of the produce the chain uses, said Chris Arnold, a Chipotle spokesman.
Jeffrey Bernstein, a analyst, noted that fast-food chains have recovered from similar foodborne illnesses in the past. But he said Chipotle's recovery will likely take longer given greater social media awareness.
Bernstein also noted that Chipotle is known for its "Food with Integrity" slogan, which makes the E. coli cases "all the more damaging."
--CNBC contributed to this article.