Clinton, 65, has been out of the public eye for the better part of December, at first because of what the State Department said was a stomach virus and later because of the concussion, which she suffered after fainting at her Washington home.
According to a spokesman, the clot was discovered in the course of a follow-up exam for the concussion at New York Presbyterian Hospital. She is being treated with anticoagulants and will remain at the hospital for the next 48 hours so doctors can monitor her response to the medication.
“Her doctors will continue to assess her condition, including other issues associated with her concussion,” Clinton spokesman Philippe Reines said in a statement. “They will determine if any further action is required.”
The State Department had said earlier that Clinton was set to resume her normal office schedule this week.
Earlier this month, the former first lady and New York senator had cited her concussion in canceling her scheduled appearance before a congressional committee investigating the Sept. 11 attack on a U.S. diplomatic facility in Benghazi, Libya, that left four Americans dead, including the ambassador.
A separate high-level investigative panel issued a scathing report blaming the State Department for security lapses. Clinton took responsibility, writing to the congressional committee that she accepted "every one" of the Accountability Review Board's 29 recommendations.
She also praised the board, saying it had offered "a clear-eyed look at serious, systematic challenges that we have already begun to fix."
Some conservatives had accused her of faking her illness to avoid testifying before the committee -- an accusation that the State Department strenuously denied.