Systems and methods are provided for authenticating aircraft communications using detected difference of on board electronics. One embodiment is a method that includes detecting a request for an exchange of data between an aircraft and an off-board system, and selecting a Line Replaceable Unit (LRU) of the aircraft based on at least one parameter of the request. The method also includes issuing a challenge to a Physically Unclonable Function (PUF) connected with at least one electronic component of the LRU, and obtaining a hardware signature based on a response of the at least one electronic component of the LRU to the challenge. The PUF derives the hardware signature from a unique physical property of the at least one electronic component. The method further includes validating the hardware signature to authenticate the request and initiate the exchange of data between the aircraft and the off-board system.