This study aims at a comparative evaluation of two recently introduced electromagnetic tracking systems under reproducible simulated operating-room (OR) conditions: the recently launched Medtronic StealthStation, Treon-EM and the NDI Aurora. We investigate if and to what extent these systems provide improved performance and stability in the presence of surgical instruments as possible sources of distortions compared with earlier reports on electromagnetic tracking technology. To investigate possible distortions under pseudo-realistic OR conditions, a large Langenbeck hook, a dental drill with its handle and an ultrasonic (US) scanhead are fixed on a special measurement rack at variable distances from the navigation sensor. The position measurements made by the Treon-EM were least affected by the presence of the instruments. The lengths of the mean deviation vectors were 0.21 mm for the Langenbeck hook, 0.23 mm for the drill with handle and 0.56 mm for the US scanhead. The Aurora was influenced by the three sources of distortion to a higher degree. A mean deviation vector of 1.44 mm length was observed in the vicinity of the Langenbeck hook, 0.53 mm length with the drill and 2.37 mm due to the US scanhead. The maximum of the root mean squared error (RMSE) for all coordinates in the presence of the Langenbeck hook was 0.3 mm for the Treon and 2.1 mm for the Aurora; the drill caused a maximum RMSE of 0.2 mm with the Treon and 1.2 mm with the Aurora. In the presence of the US scanhead, the maximum RMSE was 1.4 mm for the Treon and 5.1 mm for the Aurora. The new generation of electromagnetic tracking systems has significantly improved compared to common systems that were available in the middle of the 1990s and has reached a high level of technical development. We conclude that, in general, both systems are suitable for routine clinical application.