Volumetric digital computer-assisted reconstruction of histological sections is an attractive possibility for developmental studies. Commercial solutions are very expensive for many educational institutions. Therefore, we developed a software system for three-dimensional reconstruction of anatomical virtual models. The input data for the system are the digitized images from the histological samples of the chondrocranium of two crotalines, Bothrops jararaca and Crotalus durissus terrificus, and one colubrid, Philodryas olfersii, using a stereomicroscope connected to a digital camera. These images are then manually registered and segmented. We use computer graphics visualization algorithms such as marching cubes and ray casting to generate three-dimensional visualizations of the volumes. The results show that the digital reconstruction is as good as the manual reconstruction with the advantages of speed of reconstruction, accuracy, and flexibility to handle and study the volume. Compared with commercial options, our system has approximately the same features, and it is available free for the scientific community. © 2005 Wiley-Liss, Inc.