Using a serum sample of a bullous pemphigoid (BP) patient we have isolated a cDNA clone encoding a portion of a 180-kD polypeptide component of the hemidesmosome, the "BP180 autoantigen." The identity of the clone was confirmed by the generation of a fusion protein antibody that recognizes BP180 in both a basal epithelial cell extract of bovine tongue and extracts of human epidermal cells. Immunoelectron microscopy indicates that the 588-bp cDNA encodes a cytoplasmic fragment of BP180. Furthermore, the wide species reactivity of the fusion protein suggests that this portion of BP180 is highly conserved. In cultured human epidermal cells processed for confocal immunofluorescence microscopy, the fusion protein antibody generates a punctate cell substrate-associated staining pattern that is similar to that seen using BP230 antibodies. Using the original BP180 cDNA we have now isolated additional cDNA clones encoding approximately 1800bp of BP180 the 3' sequence of which overlaps with the sequence detailed in Guidice et al (J Clin Invest 87:734-738, 1991). Secondary structural analyses have been undertaken on the predicted amino acids encoded by the 1800bp. These suggest that the collagen-like sequences of BP180 described by Guidice et al (ibid.) are separated by a putative transmembrane region from the domain of BP180 recognized by our fusion protein antibody. Indeed, BP180 appears to belong to a relatively rare group of proteins in which the N-terminus is located in the cytoplasm and the C-terminus is extracellular. We detail some preliminary biochemical experiments in support of this hypothesis. We discuss possible functions of BP180 and BP230 in the hemidesmosome.