A system for automatic calibration of instruments (S) having varying cross-sectional dimensions within a predetermined range and having detectable elements (110, 112, 113, 114) thereon for computer-aided surgery, comprising a calibration base (C) having detectable elements (43, 44, 46, 48) secured thereto for detecting a position and an orientation thereof in space by sensors (204) connected to a position calculator (202). The calibration base is adapted to receive and to releasably secure a working shaft (100) of any of the instruments (S) and provides an abutting surface (14) for a tip (102) thereof in such a way that a position and orientation of the tip (102) of the instrument (S) secured therein is calculable when working shaft cross-section dimensions thereof are known. The position calculator (202) receives instrument data (214) and calibration data (218) from an operator through a user interface (206) and stores the instrument data (214) and calibration data (218) for subsequent calibrations.