The major soluble protein in the bovine cornea (BCP 54) has recently been identified as a class 3 aldehyde dehydrogenase. An enzymatic and even a possible structural role of this protein in the mammalian cornea has been proposed. Earlier we showed that the human cornea contains the same enzyme but with a different substrate specificity, compared to the bovine. Moreover, the enzymatic activity was harbored in the dimeric 88-kD species. Genetic variants have been found for several mammalian ocular aldehyde dehydrogenases. In this study we investigated whether such variants were also present in the human cornea by using a zymography technique for aldehyde dehydrogenase activity and immunoblotting with rabbit anti-BCP 54 and lectin staining after isoelectric focusing (IEF) and sodium dodecyl sulfate- polyacrylamide gel electrophoresis. We investigated 50 individual human corneal epithelial extracts and found one common IEF variant (n = 47) and two 'rare' IEF variants in three individuals. Analysis of these patterns indicates that the observed IEF profiles may be caused by posttranslational events.