Tracking technologies for medical Virtual or Augmented Reality (VR/AR) applications have to fulfill demanding requirements. A hybrid tracking system can merge positive attributes of different tracking technologies, for example optical and electromagnetic, and try to compensate the bad ones. The alignment of two or more tracking systems by means of transforming all measured data from different systems into one common coordinate system is a fundamental precondition. Usage and processing of time stamps assigned to each measurement is a very effective element in order to achieve a higher accuracy in the alignment procedure and during later use. The algorithms for the alignment of tracking systems can also be used for the registration of the patient, another typical task in medical VR/AR applications. This paper describes both procedures in detail, including algorithms and results from test sequences. The representative tests illustrate, that the proposed algorithms provide satisfying resu...