The pilot was to operate Flight 87, a flight with 204 passengers to Chicago. The flight was delayed while a replacement was found and the plane eventually took off at about 11:30 a.m.
In a news release, the airline said "American Airlines’ primary concern is for the safety and comfort of our passengers and crews. The company has strict policies on alcohol and substance abuse and holds its employees to the highest standards. Employees at all levels of the company are not allowed to be on duty whilst under the influence of drugs or alcohol and regular screening is carried out. Support is available for those employees who seek help for problems with substance abuse."
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No other operations were affected by the incident, AA said.
American declined to release the pilot's name Thursday.