A computer program, BrainView, is presented which has been developed to reconstruct, visualize, and evaluate three dimensional (3D) biological and medical imaging data, such as images from histological sections, confocal microscopy, or magnetic resonance tomography. The program allows the simultaneous display of three orthogonal sectional planes, i.e. the horizontal, frontal, and sagittal planes, of reconstructed data and to move interactively through the brain to optimally assess the 3D data set. Furthermore, any arbitrary sectioning plane through a data set can be visualized. Implemented warping algorithms allow the geometric normalization of data sets of different animals, modalities or developmental stages as a preprocessing for the comparative evaluation of the data. For a quantitative analysis, data sets can be segmented based on equal grey levels and the corresponding equidensities were calculated. The program works on Apple-Macintosh computers and has a user-friendly graphical interface. The BrainView program is discussed in comparison to related programs.