The State Department said the discovery of the clot stemmed from her treatment for a concussion she sustained earlier this month and was discovered during a follow-up exam Sunday.
According to Philippe Reines, a deputy assistant secretary at State, Clinton is being treated with blood thinners at New York Presbyterian Hospital, where he said she would spend the next 48 hours as doctors kept evaluating her.
"They will determine if any further action is required," Reines said. Clinton suffered a concussion earlier this month when she fainted following a bout of flu.
Details of her blood clot Sunday weren't made public, but brain injury doctors told NBC News that she may have developed a clot, perhaps a deep vein thrombosis, in her lower limbs from prolonged rest after her injury.
Such a clot would be dangerous but not necessarily life-threatening, although it is also possible Clinton could have a clot elsewhere.