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To prepare and evaluate an allopurinol mouth rinse for prophylaxis of fluorouracil-induced mucositis, 33 patients with malignant disorders, who were going to receive 5-fluorouracil containing chemotherapy, were enrolled in a placebo-controlled double-blinded randomized clinical trial. Allopurinol mouthwash (1 mg/ml) or placebo was administered 1, 2 and 3 h after chemotherapy and three consecutive nights. A questionnaire consisting of demographic parameters, medical status, quality of life survey and mucosal injury scoring table (based on World Health Organization scales for mucositis) was completed for each patient at Day 1, 3 and 7 after chemotherapy. In allopurinol group nine participants (60.0%) were female and in placebo group, 10 (66.7%) (P = 0.705). Mean ages were 56.9 +/- 10.3 and 49.5 +/- 13.8 years in allopurinol and placebo groups respectively (P = 0.107). The analysis showed that the higher education level and the use of dentures significantly reduced the occurrence of mucositis, and allopurinol mouth rinse (1 mg/ml) was ineffective in the prophylaxis of fluorouracil-induced mucositis.