Pemphigus vulgaris is an uncommon auto-immune disease which responds well to treatment with corticosteroids and azathioprine. Malakoplakia is a rare granulomatous disease associated with coliform infections and an altered cellular immune response. We report a 68-year-old female patient with pemphigus vulgaris who, after 2 years on maintenance prednisone and azathioprine immunotherapy, developed malakoplakia of the bladder associated with chronic E. coli urinary-tract infection. The malakoplakia responded well to treatment with cotrimoxazole, bethanechol chloride and ascorbic acid, combined with tapering of the corticosteroid dosage. Our patient presents an uncommon but interesting complication of long-term immunosuppressive therapy for pemphigus vulgaris.