The coexistence of antidesmoglein 3 (Dsg3) and antidesmoglein 1 (Dsg1) autoantibodies is well described in patients with pemphigus vulgaris (PV); however, there is little evidence of sequential development of these two autoantibodies. Autoantibody responses to Dsg3 and Dsg1 were studied in seven PV patients over time by enzyme‐linked immunosorbent assay, using baculovirus expressed recombinant fusion proteins. All patients had anti‐Dsg3 IgG antibodies at presentation. Two patients developed anti‐Dsg1 later in the course of the disease. The transition in autoantibody profile was associated with disease progression to generalized PV involving mucous membranes and skin in both patients; one patient initially presented with a predominantly mucosal phenotype, the other with herpetiform pemphigus‐like features. These findings demonstrate that there is an extension of autoimmune response from anti‐Dsg3 only to both anti‐Dsg3 and anti‐Dsg1 in some patients, which is associated with an alteration in clinical expression in PV.