Eyewitnesses believe the man was running for a downtown No. 1 train at the 66th Street station when he disappeared after hitting the train doors.
He is thought to have been pinned between the train and the platform and dragged a short distance.
Firefighters were able to free the man, who eyewitness describe as a younger man in his 30s.
Investigators are now trying to determine the exact cause of the accident.
He was taken to New York Presbyterian Hospital with head and pelvic injuries, and is expected to survive.
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