In human epidermis and other cornified squamous epithelia, corneodesmosin is located in the desmosomes of the upper living layers, and in related structures of the cornified layers, the corneodesmosomes. During maturation of the cornified layers, the protein undergoes a series of cleavages, thought to be a prerequisite of desquamation. Partial amino acid sequencing of corneodesmosin fragments suggested that it is related to the product of the S gene, previously identified in the human major histocompatibility complex. We report the expression cloning of corneodesmosin cDNA from a human epidermis library screened with monoclonal antibodies. Sequencing demonstrated that corneodesmosin is really the product of the S gene. However, analysis of 20 alleles of the gene revealed that its product is 27 amino acids longer than initially reported. Two additional polymorphic sites were described, and the position of the unique intron was ascertained. Corneodesmosin cDNA expression in COS-7 cells led to secretion of the protein. Precise epitope mapping allowed further characterization of the molecular forms of corneodesmosin present in the most superficial cornified layers, where fragments corresponding to the central region of the protein were detected. This indicated a cleavage of the N- and C-terminal domains of corneodesmosin before desquamation. These serine- and glycine-rich domains are proposed to mediate an adhesive function.