A new method is presented for mapping the motor cortex by transcranial magnetic stimulation in which the position of the stimulation coil on the scalp is measured using a 3D digitizer. The reproducibility of the method was tested by mapping 3 times the left abductor digiti minimi of 6 right-handed subjects and calculating the position of the centre of gravity (CoG), the area and volume of the individual maps. For individual maps, the coordinates of the CoG were found to be reproducible within +/-3 mm and the map areas and normalized volumes to within +/-20%, when the induced current flows anteriorly. Six more subjects were mapped to estimate interindividual variability of the position of the CoG. The method's ability to differentiate the cortical representation of two close muscles was successfully tested by mapping the flexor carpi radialis and the biceps brachii in another subject. Coordinates are given in a Cartesian frame of reference defined by the two tragi and the nasion. This feature will facilitate the comparison of results and their superposition on MR images.