The 66-year-old was found in a fetal position, semi-conscious and suffering from neck injuries in his jail cell at the Manhattan Metropolitan Correctional Center.
Investigators are now looking into whether Epstein was assaulted or if it was a suicide attempt.
Court documents earlier this month showed Epstein is facing charges related to creating a network that allowed him to sexually exploit and abuse underage girls.
The alleged victims were as young as 14 at the time.
Authorities say he paid underage girls for massages and then molested them at his homes in Florida and New York in the early 2000s.
A federal judge ruled Epstein would be held in custody without bail.