Endoscopic Ultrasound (EUS) features flexible endoscopes equipped with a radial or linear array scanhead allowing high resolution examination of organs adjacent to the upper gastrointestinal tract. An optical system based on fibre-glass or a CCD-chip allows additional orientation. However, 3-dimensional orientation and correct identification of the various anatomical structures may be difficult. It therefore seems desirable to merge real-time US images with high resolution CT or MR images acquired prior to EUS to simplify navigation during the intervention. The additional information provided by CT or MR images might facilitate diagnosis of tumors and, ultimately, guided puncture of suspicious lesions. We built a grid with 15 plastic spheres and measured their positions relatively to five fiducial markers placed on the top of the grid. For this measurement we used an optical tracking system (OTS) (Polaris, NDI, Can). Two sensors of an electromagnetic tracking system (EMTS) (Aurora, NDI, Can) were mounted on a flexible endoscope (Pentax GG 38 UX, USA) to enable a free hand ultrasound calibration. To determine the position of the plastic spheres in the emitter coordinate system of the EMTS we applied a point-to-point registration (Horn) using the coordinates of the fiducial markers in both coordinate systems (OTS and EMTS). For the transformation between EMTS to the CT space the Horn algorithm was adopted again using the fiducial markers. Visualization was enabled by the use of the AVW-4.0 library (Biomedical Imaging Resource, Mayo Clinic, Rochester/MN, USA). To evaluate the suitability of our new navigation system we measured the Fiducial Registration Error (FRE) of the diverse registrations and the Target Registration Error (TRE) for the complete transformation from the US space to the CT space. The FRE for the ultrasound calibration amounted to 4.3 mm ± 4.2 mm, resulting from 10 calibration procedures. For the transformation from the OTS reference system to the EMTS emitter space we found an average FRE of 0.8 mm ± 0.2 mm. The FRE for the CT registration was 1.0 mm ± 0.3 mm. The TRE was found to be 3.8 mm ± 1.3 mm if we target the same spheres which where used for the calibration procedure. A movement of the phantom results in higher TREs because of the orientation sensitivity of the sensor. In that case the TRE in the area where the biopsy is supposed to be taken place was found to be 7.9 mm ± 3.2 mm. Our system provides the interventionist with additional information about position and orientation of the used flexible instrument. Additionally, it improves the marksmanship of biopsies. The use of the miniaturized EMTS enables for the first time the navigation of flexible instruments in this way. For the successful application of navigation systems in interventional radiology, an accuracy in the range of 5 mm is desirable. The accuracy of the localization of a point in CT space are just 3 mm too high as required. One of the possibilities to overcome this difference is to mount the two sensors in such a way that the interference of their electromagnetic fields is minimized. A considerable restraint constitutes the small characteristic volume (360mm x 600mm x 600mm), which requires for most application an additional optical system.