Image-guided surgical navigation is on the rise in many different areas of modern medicine and is already an established standard in some disciplines like ear nose and throat (ENT) or maxillofacial surgery. When evaluating surgical navigation systems the absolute accuracy of the device is of major concern to the surgeon. The following work presents two different ways of measuring the accuracy of surgical navigation systems using the example of the KARL STORZ Navigation Panel Unit (NPU). According to these protocols the FDA approval of the NPU navigation system was prepared. In a first series of experiments the accuracy under realistic surgical conditions is evaluated with a phantom of a human head, which is manufactured in rapid-prototyping processes. In another series of experiments a custom registration board is used, which provides means to evaluate the accuracy under optimal conditions and also allows further measurements regarding the registration error, that are not possible with the phantom. In the experiments an accuracy of 1.44 mm ± 0.18 mm was measured in the surgical setup and 0.63 mm ± 0.07 mm under ideal conditions.