In pre-market trading, shares were down about 4% and at the lowest level in about one year.
On Monday, a Boston College official confirmed to Business Insider that several BC students and members of the men's basketball team had complained of gastrointestinal symptoms after they all ate at Chipotle.
The company told Business Insider that it had no indication the new incident in Boston was linked to previous ones, and had no confirmed cases of E. coli connected to Chipotle in Massachusetts.
This came as the Centers for Diseases Control and Prevention (CDC) continued to investigate new cases of E. coli linked to Chipotle and announced on Friday.
After the CDC's announcement on Friday, Chipotle said in a regulatory filing that it expects fourth-quarter sales to fall by between 8% and 11%.
And to start the week, Chipotle received several price-target downgrades from analysts, although most still believed in the long-term profitability of the restaurant chain.
In the last three months, Chipotle shares have dropped more than 20%. Before the CDC started looking into E. coli cases, there had been separate investigations of norovirus in California and salmonella in Minnesota linked to Chipotle earlier this year.
This chart shows the drop in shares pre-market on Tuesday:
