In this article a new navigated drill system for computer assisted ear, nose and throat (ENT) surgery is presented. The navigated drill and the microscope probe are part of a surgical navigation system for ENT-surgery. In particular, the accuracy of the new navigated drill is compared to an existing navigated drill experimentally under conditions close to the surgical workflow. For the technical accuracy experiment, the new navigated drill in combination with the new microscope probe and a particular navigated measurement board have been integrated, together with the current navigated drill, in a navigation system by a special navigation software with measuring function, based on a standard ENT navigation software. The developed navigated measurement board provided the implementation of reproducible experiments and the direct accuracy comparison of the two navigated instruments under the same conditions. Thereby, N = 15 accuracy experiments are performed with both navigated drill systems with three possible tracker positions. The distance between the planned and the touched points were calculated and compared. The average distances from the planned points to the touched points with the new navigated drill is in the left tracker position 1.10 mm, in the middle tracker position 1.14 mm and in the right tracker position 1.59 mm. In comparison to the existing drill, the new navigated drill, measured with each tracker position, is 0.62 mm more accurate.