Pemphigus vulgaris is an autoimmune blistering disease caused by autoantibodies against desmoglein 3, a member of the desmosomal cadherin family. These autoantibodies recognize conformation-dependent epitopes on desmoglein 3. In this study we attempted to map the conformational epitopes of desmoglein 3 in pemphigus vulgaris using recombinant desmoglein 3 produced by the baculovirus expression system. We developed a series of domain-swapped molecules between desmoglein 3 and desmoglein 1, which have similar structures but distinct epitopes. These were developed by substituting deleted segmental regions of desmoglein 3 by the corresponding desmoglein 1. Thus domain-swapped molecules containing desmoglein 3 residues 1–403, 1–161, 163–566, and 405–566 were constructed and used as competitors for competition enzyme-linked immunosorbent assay against the entire extracellular domain of desmoglein 3 with 25 pemphigus vulgaris sera. Considering more than 50% absorption as significant, residues 1–403 and 1–161 showed significant absorption in 24 out of 25 (96%) and 18 out of 25 (72%) pemphigus vulgaris sera, respectively, whereas only one serum and no sera showed significant absorption by residues 163–566 and 405–566, respectively. Furthermore, no apparent change in their major epitopes was seen during the time course in four pemphigus vulgaris cases tested. These findings indicate that the domain-swapping approach is useful for conformational epitope mapping in pemphigus and that amino-terminal residues 1–161, which are considered to include a region essential for cell-cell adhesion in cadherins, contain the critical residues of the conformational epitope of desmoglein 3 recognized by the autoantibodies in pemphigus vulgaris sera.