Mrs Clinton's doctors discovered the clot yesterday during a follow-up exam, her spokesman, Philippe Reines, said.
He said the US Secretary of State was being treated with anti-coagulants and would remain at New York Presbyterian Hospital for at least the next 48 hours.
Mrs 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.
She was forced to cancel a trip to North Africa and the Middle East that had been planned for the next week.
The seriousness of a blood clot "depends on where it is", said Dr Gholam Motamedi, a neurologist at Georgetown University Medical Centre.
Clots in the legs are a common risk after someone has been bedridden, as Mrs Clinton may have been for a time after her concussion. Those are "no big deal" and are treated with six months of blood thinners to allow them to dissolve on their own and to prevent further clots from forming.
A clot in a lung or the brain is more serious. Lung clots -- pulmonary embolisms -- can be fatal, and a clot in the brain can cause a stroke, Dr Motamedi said.
Keeping her in the hospital for a couple of days could allow doctors to perform more tests to determine why the clot formed, and to rule out a heart problem or other condition that may have led to it.
Mrs Clinton was forced to cancel testimony before Congress about a scathing report into the September 11 attack on the US consulate 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.
Mrs Clinton took responsibility for the incident before the report was released, but she was not blamed.
Some conservative commentators suggested she was faking the gravity of her illness and concussion to avoid testifying, although State Department officials vehemently denied that was the case.
The former first lady and senator, who had always planned to step down as America's top diplomat in January, is known for her gruelling travel schedule. She is the most travelled secretary of state in history, having visited 112 countries while in the job.
Mrs Clinton is considered a front-runner for the Democratic presidential nomination in 2016, although she has not announced plans to run.