The upper layers of mammalian epidermis contain citrulline-containing proteins formed by enzymatic deimination of arginine residues. To study the role of protein deimination in epidermal differentiation, we identified deiminated proteins extracted from human epidermis. Major deiminated proteins were identified as partially degraded keratin K1, while those from keratin K10 and a highly heterogeneous mixture of deiminated filaggrin isomers were detected as minor components. Deiminated keratins were recovered in a fraction enriched with keratins from the cornified layers. The subsequent immunohistochemical study showed that deiminated proteins were localized mainly in the lowermost cornified layer, but not in the granular layer. These data suggested that partially degraded/disulfide-cross-linked keratin K1 was preferentially deiminated during the terminal stages of epidermal differentiation. We therefore speculated that the protein deimination might influence the interaction of basic K1 with its acidic partner K10, pre-existent K5/K14 networks or keratin-associated protein filaggrin.