Clinton's doctors discovered the clot Sunday while performing a follow-up exam, her spokesman, Philippe Reines, said.
He would not elaborate on the location of the clot but said Clinton is being treated with anti-coagulants and would remain at New York-Presbyterian Hospital for at least the next 48 hours so doctors can monitor the medication.
"Her doctors will continue to assess her condition, including other issues associated with her concussion," Reines said in a statement. "They will determine if any further action is required."
Clinton, 65, fell and suffered a concussion while at home alone in mid-December as she recovered from a stomach virus that left her severely dehydrated. The concussion was diagnosed Dec. 13 and Clinton was forced to cancel a trip to North Africa and the Middle East that had been planned for the next week.
Clinton also was forced to cancel Dec. 20 testimony before Congress about a scathing report into the Sept. 11 attack on the U.S. diplomatic mission in Benghazi, Libya, that killed Ambassador Chris Stevens and three other Americans.
The report found that serious failures of leadership and management in two State Department bureaus were to blame for insufficient security at the facility.
Clinton took responsibility for the incident before the report was released, but she was not blamed.
Some conservative commentators suggested Clinton was faking the seriousness of her illness and concussion to avoid testifying, although State Department officials denied that was the case.
Lawmakers at the hearings -- including Sen. John Kerry, D-Mass., the Senate Foreign Relations Committee chairman who has been nominated by President Barack Obama to succeed Clinton -- offered her their best wishes.
The former first lady and senator, who had always planned to step down as America's top diplomat in January, is known for her grueling travel schedule. She is the most traveled secretary of state in history, having visited 112 countries while in the job.
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