We have identified a spliced mRNA transcript of CD20 (named D393-CD20) which was associated with resistance to RTX in primary B cell from patients with lymphoma and leukaemia. In the present work, we wished to investigate whether D393-CD20 variant was expressed by B cells from patients with pemphigus. Ten patients with bullous pemphigoid and twenty-five patients with pemphigus were included. All patients were responder to conventional immunosuppressive agents or rituximab (n = 11). Efficacy of B-cell activation by pokeweed mitogen was assessed by CD86 expression using a FACS Canto II flow cytometer. mRNA CD20 expression study was then performed using RT-PCR assay allowing first to discriminate wild-type (wt)-CD20 and D393-CD20 transcript. Although wt-CD20 expression was always detected, we were unable to detect D393-CD20, even after B-cell activation or RTX treatment. Our results suggest that D393-CD20 transcript may be a molecular marker of B-cell malignancies rather than autoimmune disease like pemphigus. Further study of RTX non-responders or non-escaping PV patients is thus still required to appreciate whether D393-CD20 expression may be detected under the pressure of RTX therapy.