In this study we investigated the properties of corneal aldehyde dehydrogenase (ALDH) in keratoconus corneas using various electrophoretic techniques combined with immunochemical and zymographic identification. Normal corneas and other pathologic corneal buttons obtained during keratoplastic surgery were used as a control. A significant (p < 0.001) lower enzymatic activity was found in keratoconus epithelial extracts (3.1 ± 2.1 IU/mg protein) compared with normal controls (5.5 ± 2.6 IU/mg protein), whereas no significant differences were observed in the stromal and endothelial extracts. No significant differences were observed for the corneal ALDH thermolability behavior, nor did any marked changes occur in the position of the 54- and 88-kDa species when comparing the pathologic corneas and normal controls. On the other hand, isoelectric focusing analysis showed a different pattern for the pathologic corneas as compared with controls. Moreover, native-polyacrylamide gel electrophoresis analysis showed that normal corneas exhibit three bands, whereas keratoconus and other pathologic corneas only show two bands. The shift from the three-band pattern to the two-band pattern could be reproduced in vitro using reducing agents, such as glutathione.