A calibration system for the calibration of a surgical instrument, comprises a surgical instrument having a working shaft. A clamp has a first trackable member and is releasably connected to the surgical instrument such that an orientation relation between the clamp and the working shaft of the instrument is known. A base is separated from the clamp and has a second trackable member and a positioning portion being tracked for position. A sensor unit tracks the first and second trackable members. A calibration unit calibrates the surgical instrument by initializing the orientation relation between the clamp and the working shaft from the tracking data to obtain an orientation of the working shaft, and by setting a position for the working shaft with respect to the first trackable member by relating the orientation of the working shaft to the position of the positioning portion when the working shaft contacts the positioning portion.