For the commissioning and operation of the German Heavy Ion Therapy Project a quality assurance program was developed and successfully applied. The complete radiotherapy process using heavy ions was carefully analyzed and divided into three areas related to beam delivery and control, safety-interlock system and medical physics issues. In this paper, the medical physics issues are addressed. Since the irradiation with heavy ions is a nonstandard modality, new concepts and ion specific tests were developed. As far as possible, national and international standard specifications for radiotherapy were adopted. For each aspect, a performance characteristic and a corresponding acceptance test were introduced. In addition, test characteristics for the constancy tests were established. For all tests, intervention thresholds and test frequencies were specified. Using the described protocol of acceptance tests, the commissioning was passed successfully. The heavy ion irradiation facility was approved by the governmental authorities on the basis of these test results. During clinical operation, constancy tests are performed at the beginning of each treatment period, in order to maintain the quality found during the acceptance tests. Up to now, 48 patients have been treated within 6 treatment periods of 4 weeks each. The concepts used and the tests developed for the quality assurance program may serve as an example of how to introduce systematically a quality assurance program for a new treatment modality.