Computer-assisted analysis of endothelial morphology provides useful indices of cell shape and size which appear to correlate to the monolayer's functional status. In this study morphometric data obtained by wide-field specular microscopy of in situ corneal endothelia are compared to data obtained by alizarin red S staining of excised corneas. Both human donor corneas and rabbit corneas were studied. The results of the study indicate that considerable (14%) cell shrinkage occurs in rabbit endothelia following staining. Associated with this cell shrinkage is a normalization of cell area which is manifest as a significant (P less than 0.001) decrease in the coefficient of variation of cell area. The percentage of hexagonal cells, however, remains unchanged. These changes were not mitigated by lowering the osmolality of the saline rinse following staining or by minimizing evaporation by placing a drop of silicone oil on the stained button. In human tissue no significant differences in cell area or cell shape were noted in comparing morphometric data obtained by staining to that obtained from specular microscopy. Useful morphometric data can be obtained by alizarin staining. This technique combined with cell morphometric analysis could provide valuable data in corneas whose lack of clarity limits or precludes specular microscopy. Caution, however, must be exercised in comparing morphometric data by this method to those obtained in situ for rabbit tissue.