A human epidermal keratinocyte lambda gt11 recombinant cDNA library was screened with a 0.45-kb cDNA that was generated by polymerase chain reaction (PCR) amplification of a segment of human bullous pemphigoid (BP) antigen mRNA. The screen yielded five clones, the largest one, pcBPA-4, being 2.3 kb in size. The pcBPA-4 cDNA hybridized in Northern analyses with an approximately 9-kb mRNA from cultured keratinocytes, whereas no hybridization signal was detected with RNA from human skin fibroblast, fibrosarcoma HT-1080 cells, or amniotic epithelial WISH cell cultures. Nucleotide sequencing of pcBPA-4 revealed an open reading frame encoding a putative polypeptide of 447 amino acids. This polypeptide showed 88% homology with corresponding mouse BP antigen sequences, and a region of it was identical to a segment in previously published human BP antigen sequences. The 2.3-kb cDNA isolated here was different from a previously published human BP antigen cDNA, in that the open reading frame coded for 264 additional amino acids at the carboxyl end of the putative polypeptide. Known human BP antigen amino acid sequences, compared with mouse sequences, were predicted to be moderately divergent with a unit of evolutionary period (UEP) of 4.5 millions of years (MY). Southern hybridizations suggested that the BP antigen gene (BPAG1) is present as a single copy in the human genome. Southern analyses also revealed the presence of a StuI restriction fragment length polymorphism that can be used for linkage analyses to study the inheritance of a particular BPAG1 allele and a heritable cutaneous disorder affecting the basement membrane zone, such as epidermolysis bullosa.