Jordan Gardner, 28, was met by police on Sunday when his flight landed in Charlotte, North Carolina, and was arrested for "damaging a plane".
Mid-flight he pulled down his pants, arched his back and urinated on the floor, witnesses say.
Passengers notified a flight attendant, who promptly sent Gardner to the bathroom and then used soda water to clean the mess. Unfortunately the pungent smell remained and passengers had to put up with it for the rest of the flight, about four hours.
Gardner failed to return from the bathroom after 15 minutes and when a flight attendant opened the door, she found him lying on the floor of the bathroom.
Gardner told police he had had two double shots of vodka at the San Francisco Airport bar before the flight. But police said they could still smell alcohol on his breath 11 hours after the flight took off.
He told them the smell "may have been caused by the gum he was chewing," and that he did not remember urinating on the plane, passing out in the bathroom, or anything about the flight itself.
He now faces a criminal complaint of damaging an aircraft.
An American Airlines spokesman said they asked police to meet the flight on its arrival at Charlotte 'due to a disturbance on on the aircraft', but referred all questions to the FBI.
The FBI said Gardner had a multi-state criminal history, with charges and arrests for battery, trespassing, auto theft, passing bad checks, being under the influence, and vandalism.
