Abstract The aim of the present study was to evaluate the effect of systemic administration of probiotics (PROB) on the progression of experimentally induced oral and intestinal mucositis in rats immunosuppressed by chemotherapy (5-fluorouracil: 5-FU). Twenty-four rats were divided into the following groups (n=6): GC (control), GPROB, G5FU and G5-FU/PROB. Groups GPROB and G5-FU/PROB received 1 g of probiotic incorporated into each 100 g of feed (Bacillus subtilis, Bifidobacterium bifidum, Enterococcus faecium and Lactobacilllus acidophilus), beginning 30 days before oral mucositis induction. Groups G5FU and G5-FU/PROB received 60 mg/kg of 5-FU on days 0 and 2. The left oral mucosa of each animal was irritated by mechanical trauma (days 1 and 2). On days 3 and 7, three animals from each group were sacrificed, and their oral mucosa and small intestine were biopsied and processed for histopathological analysis. Groups G5-FU and G5-FU/PROB showed ulcerated oral lesions at day 3, with progression in group G5-FU and regression in group G5-FU/PROB at day 7. Histologically, less severe signs of inflammation in the oral mucosa were observed in group G5-FU/PROB than in group G5-FU. Regarding the intestine, villus-related defects of lesser magnitude were observed in group G5-FU/PROB, compared with group G5-FU. Group GPROB showed greater villus height than group GC. It can be concluded that probiotic supplementation reduced oral and intestinal inflammation in immunosuppressed rats with experimentally induced mucositis, and may protect the intestine from changes induced by chemotherapy, thus contributing to overall health.