Dose uniformity of a scanning ion implanter is determined. A base beam current is measured at the beginning and/or the end of a complete scan over the whole substrate area. This base beam current is measured at a time when the measurement should be unaffected by outgassing from a substrate being implanted and a base dose distribution map is then calculated for the scan in question. During the scan itself beam instability events are detected and the magnitude and position in the scan of the detected instability events is measured. Corresponding deviations in the calculated base dose map are determined and subtracted from the previously calculated base dose distribution map to provide a corrected distribution map. By determining overall dose uniformity substractively in this way, good overall accuracy can be obtained with lesser accuracy in the measurement of the beam instability events.