Human corneas from normal (healthy) donors and patients with keratoconus were either metabolically labelled under organ culture conditions or investigated without preincubation. The sulfated proteoglycans were isolated from a 4 M guanidinium chloride/2% Triton X 100 extract. Two predominant proteoglycans were obtained from normal cornea after digestion of total sulfated proteoglycans with chondroitin ABC-lyase or endo-beta-galactosidase. One had an overall mass of 150 kDa, two dermatan sulfate chains (Mr approximately 50 kDa) with an iduronic acid content of 24%-28% and, after chondroitin ABC-lyase digestion, a core protein of 48 kDa. The other proteoglycan had an overall mass of 110 kDa, one keratan sulfate chain of approximately 60 kDa and, following endo-beta-galactosidase (keratanase) digestion, a core protein of 46 kDa. Each proteoglycan population was further fractionated into two subpopulations by chromatography on concanavalin A-Sepharose. The dermatan sulfate- and keratan sulfate-containing proteoglycans isolated from keratan and healthy cornea had comparable Mr values and core proteins with identical molecular weights, but the ratio of dermatan sulfate/keratan sulfate proteoglycan was increased in keratoconic cornea and the keratan sulfate chains of two keratan sulfate proteoglycans from keratoconic cornea were considerably shorter (Mr 44 and 33 kDa) than those from normal corneas.