The method involves placing a probe e.g. catheter (20), having a position sensor and an ultrasonic transducer in a test fixture. A position signal generated by the sensor is measured while the transducer is in alignment with an ultrasonic target, to determine an orientation of the probe in a frame of reference of the fixture. Calibration data is determined for the probe in responsive to the orientation of the probe. An independent claim is also included for an apparatus for calibrating a probe having a position sensor and an ultrasonic transducer.