Two-dimensional electrophoretic maps of extracts from eleven normal and eleven keratoconus corneas were compared. Of the eleven corneas analyzed, eight were pooled and the remaining three were analyzed individually. Several differences were demonstrated between electrophoretic patterns of normal and keratoconus corneas. In keratoconus corneas, 1) two abnormal components (MW 54kD and 26kD) were observed; 2) three normal corneal components (MW 12kD, 14kD, and 39kD) were present in significantly higher amounts; and 3) three normal corneal proteins (MW 66kD, 55kD, and 13kD) were present in reduced amounts. The molecular weight and isoelectric point of one of the normal corneal proteins that we found to be reduced in keratoconus corneas were close to that of a subunit of prolyl-4-hydroxylase, an enzyme required for hydroxylation of proline residues of collagen. The possibility the abnormal proteins detected in the keratoconus corneas were derived from those normal corneal proteins which were absent or were present in reduced amounts in the keratoconus corneas remains to be established. This study may provide protein markers for elucidation of the biochemical abnormality in keratoconus.