The major antibody binding regions of desmoglein 1 (Dsg1) in pemphigus foliaceus and pemphigus vulgaris were examined using cDNA-encoded fusion proteins combining glutathione S-transferase with various domains of bovine Dsg1, namely, the extracellular regions EC1-2, EC3-5, EC1-5, and the entire intracellular region IC. In immunoblot analyses using these fusion proteins, EC1-2, as well as EC1-5, which comprises EC1-2, were recognized by 50% of the sporadic pemphigus foliaceus sera and 45% of Brazilian pemphigus foliaceus sera that reacted with Dsg1 in immunoblotting of bovine desmosome preparations. None of these fusion proteins reacted with any sera of pemphigus vulgaris. None of these sera showed reactivity with EC3-5. In contrast, the IC domain was recognized by 91% of pemphigus vulgaris sera reactive with Dsg1 in bovine desmosome preparations, and by certain pemphigus foliaceus and Brazilian pemphigus foliaceus sera. These results indicate that major epitopes of Dsg1 recognized by pemphigus foliaceus and Brazilian pemphigus foliaceus sera are located in the extracellular amino-terminal domain EC1-2, and that sera of the Dsg1-positive pemphigus vulgaris contain antibodies against the intracellular domain, which may not play a pathogenic role. Possible reasons for this selectivity of antigen binding site are discussed.