Systems and methods for encrypting the output of a card reader in a card authentication system are provided. In one embodiment, the invention relates to a method for reading a data card having an intrinsic magnetic characteristic and recorded data on the data card using a read head including a magnetic sensor having a housing, an analog to digital converter located within the housing and a processor located within the housing, the method including generating an analog signal indicative of the intrinsic magnetic characteristic and the recorded data of the data card, converting the analog signal into a digital signal, generating a magnetic fingerprint based on the intrinsic magnetic characteristic from the digital signal, extracting the recorded data from the digital signal, encrypting at least a portion of the recorded data, storing the magnetic fingerprint and the recorded data, and outputting the encrypted at least the portion of the recorded data.