High precision acquisition of atmospheric parameters from the air or space by means of lidar requires accurate knowledge of laser pointing. Discrepancies between the assumed and actual pointing can introduce large errors due to the Doppler effect or a wrongly assumed air pressure at ground level. In this paper, a method for precisely quantifying these discrepancies for airborne and spaceborne lidar systems is presented. The method is based on the comparison of ground elevations derived from the lidar ranging data with high-resolution topography data obtained from a digital elevation model and allows for the derivation of the lateral and longitudinal deviation of the laser beam propagation direction. The applicability of the technique is demonstrated by using experimental data from an airborne lidar system, confirming that geo-referencing of the lidar ground spot trace with an uncertainty of less than 10 m with respect to the used digital elevation model (DEM) can be obtained.