Clinton's spokesman, Philippe Reines, said her doctors discovered the clot during a follow-up exam Sunday. Reines said Clinton is being treated with anti-coagulants and is at New York-Presbyterian Hospital so they can monitor the medication over the next 48 hours.
Reines said doctors will continue to assess Clinton's condition, including "other issues associated with her concussion."
Earlier this month, Clinton fainted and hit her head after contracting a stomach virus. Aides said she became dehydrated, then fainted, fell and hit her head. She was diagnosed with a concussion Dec. 13.
Clinton's illness led her to cancel an overseas trip and scheduled testimony before Congress about the attack on the U.S. Consulate in Libya.
She was scheduled to return to work this week.
The Associated Press contributed to this report.