There are several approaches of extracting three dimensional (3D) morphometrical information from biological fine structures, computer 3D reconstruction using thin serial sections, stereologica1 analysis of random thin section images, reconstruction from the results obtained by Fourier analysis of continuously tilted images, and so on. We have developed a computer analysis method of HVEM stereo images of thick biological specimens. Each method has advantages and disadvantages and one can choose one or other method according to the nature of samples and/or the nature of the required information.In our method, stereo paired electron micrographs are processed to produce skeletonized images, they are automatically traced, and the z coordinates of the given specimen points are calculated from the parallaxes between the two tilted images and the tilt angle.