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After hematopoietic cell transplantation, a variety of complications can occur, including chronic graft-versus-host disease (GVHD), with 25% to 70% of these involving the oral cavity. Those lesions, as well as oral involvement of autoimmune mucocutaneous diseases, might present as painful, erythematous, and ulcerative oral lesions. Management includes topical and systemic immunosuppressive agents, including systemic azathioprine (AZA). The purpose of this study was to evaluate the efficacy of topical AZA in chronic oral GVHD and in oral autoimmune diseases in a series of patients.Four men and 2 women with GVHD and 2 men with autoimmune vesiculo-ulcerative oral lesions were treated with topical AZA. A rinse of 5 mL of 5 mg/mL AZA in methylcellulose were rinsed 3 to 4 times daily for over 1 minute and expectorated, or a gel in the same concentration in 3% methylcellulose was topically applied. The outcome was evaluated separately for total ulcer size, assessment of the erythema, and severity of pain by using a visual analogue scale. Global estimated improvements represented a proportional combined improvement of ulcers, erythema, and pain.The mean estimated global improvement for 6 patients with GVHD who used AZA rinse was 60% in a mean of 16.67 weeks. Ulcers improved by 58%, erythema by 55%, and pain was reduced by 63%. Two patients with oral lesions of vesiculo-ulcerative diseases (1 AZA rinse and 1 topical gel) improved by 95% and 96%, respectively, in 3 months. One patient with GVHD applied topical AZA gel in addition to mouthrinses, and a 29% estimated global improvement was achieved in addition to 50% of improvement achieved with AZA mouthrinses. The observed effect of topical AZA suggests that it can be used for management of oral immune-mediated inflammatory conditions, and for patients who are provided with systemic immunosuppressives it can allow control of oral findings with lower systemic dosing. The therapeutic potential of topical AZA as mouthrinse versus topical applications and the most effective concentration should be further investigated.