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Objective. We questioned whether the position of the dynamic reference frame (DRF) influences the application accuracy in electromagnetically navigated cranial procedures. A carrier for an electromagnetic DRF was developed, which could be fixed at the posterior edge of the vomer near the center of the head. This nasopharyngeal DRF was compared with a standard DRF fixed to the surface of the forehead. Methods. Image coordinates and real-world coordinates were co-registered and the total target error (TTE) was measured in the frontal and the lateral skull base of formalin fixed human head. At each anatomical site, 10 targets served for TTE determinations and 5 different fiducial combinations were used for registration. Results. With the nasopharyngeal DRF, lower TTE values (2.8 ± 1.4 mm; mean ± SD) were observed when compared with the forehead DRF (3.7 ± 2.8 mm; P = .004). TTEs of both anatomical sites investigated were significantly lower when using the nasopharyngeal DRF (frontal skull base 3.4 vs 2.1 mm, P = .005 and lateral skull base 3.9 vs 3.5 mm, P = .013) than with the standard forehead mounted one. Conclusion. Positioning the DRF in the center of the head significantly improved the application accuracy of targets in the skull base with electromagnetic navigation by 25%. [ABSTRACT FROM PUBLISHER]