Pemphigus vulgaris (PV) is an autoimmune blistering disease characterized by circulating pathogenic IgG antibodies against desmoglein 3 (Dsg3). The purpose of this study was to develop chimeric molecules for specific recognition and elimination of autoimmune B cells in PV. Mouse hybridoma cell lines producing anti‐Dsg3 antibody (5H10, 12A2) were developed as an in vitro model system for targeting B cells. Dsg3‐GFP, a baculoprotein containing the entire extracellular domain of Dsg3 fused with green fluorescence protein, recognized and targeted the hybridoma cells through their surface immunoglobulin receptors in an antigen‐specific way. The epitopes of these monoclonal antibodies were mapped on the amino terminal EC1 and part of EC2, a region considered functionally important in cadherins. Chimeric toxin molecules containing the mapped region (Dsg3ΔN1) and modified Pseudomonas exotoxin were produced in bacteria (Dsg3ΔN1‐PE40‐KDEL, PE37‐Dsg3ΔN1‐KDEL) and tested in vitro on hybridoma cell lines. The chimeric toxins, but not Dsg3ΔN1 alone, showed dose‐dependent toxic activity with a reduction in hybridoma cell number to 40–60% of toxin‐negative control cultures, compared with little or no effect on anti‐Dsg3‐negative hybridoma cells. Furthermore, these toxins showed toxic effects on anti‐Dsg3 IgG‐producing B cells from Dsg3ΔN1‐immunized mice, with a 60% reduction in cell number compared with Dsg3ΔN1 alone. Thus, specific recognition and targeting of antigen‐specific B cells in PV was demonstrated; this strategy may hold promise as a future therapeutic option for PV and other autoimmune diseases.