The US Secretary of State's doctors found the clot while performing a follow-up examination.
Her spokesman, Philippe Reines, would not give the location of the clot but said Mrs Clinton is 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.
The concussion was diagnosed on December 13 and Mrs Clinton was forced to cancel a trip to North Africa and the Middle East 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 who was not involved in Mrs Clinton's care.
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. A clot in a lung or the brain is more serious. Lung clots or pulmonary embolisms can be deadly, and a clot in the brain can cause a stroke, Dr Motamedi said.
Keeping Mrs Clinton in the hospital will let doctors 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, he added.
Mrs Clinton was forced to cancel testimony before Congress about a scathing report into the September 11 attack on the US diplomatic mission in Benghazi in Libya that killed Ambassador Chris Stevens and three other Americans.
The report found serious failures of leadership and management in State Department bureaux. Mrs Clinton took responsibility for the incident, but was not blamed. Before the discovery of the clot she was expected to return to work this week.
She is considered a front-runner for the Democratic presidential nomination in 2016, although she has not said she will run.