Abstract: A pilot authentication system for commercial and non-commercial aircraft is provided. A processor containing a database of digitized fingerprints of individuals authorized to control a given aircraft is located in the aircraft and in communication with the aircraft's avionics computer. A plurality of sensors, including fingerprint and biometric sensors, sample the fingerprints and biometric information at an individual at the controls of the aircraft. The processor compares the sampled fingerprints to the database of authorized individuals, determining whether an unauthorized individual is at the controls of the aircraft. Using the biometric information, the processor also determines whether a pilot is experiencing physical distress while at the controls of the aircraft. Further, the processor determines whether the aircraft is in motion and is not being controlled by either an authorized pilot or the aircraft's autopilot.