An auto alignment pad printer for transferring print to an associated object includes a frame, a fixture for supporting the associated object and a cliché operably mounted to the frame. The cliché includes at least one etched region and is adapted to receive ink in the etched region. An ink cup is configured to deposit ink into the etched region. A pad applicator includes a pad support having at least one pad thereon. The pad is adapted to move into and out of contact with the etched region to receive ink from the etched region and to contact an object to transfer the received ink to the object. A pad applicator alignment assembly includes a first set of cooperating projections and receivers mounted to the pad applicator and to the cliché and/or the frame near to the cliché, and a second set of cooperating projections and receivers mounted to the pad applicator and to the fixture for supporting the object. The first set of cooperating projections and receivers are configured to position the pad for precise movement into contact with the cliché to receive ink from the cliché. The second set of cooperating projections and receivers are configured to position the pad for precise movement into contact with the object to transfer the received ink to the associated object.