Introduction: Intestinal mucositis is the most prevalent side effect of antineoplastic drug 5-flurouoracil (5-FU). Probiotics are live microorganisms that improve intestinal immune regulation. So, probiotics might have a beneficial effect to reduce the chemotherapy-induced entero-toxicity. Aim: This study aimed to assess mucositis induced by 5-FU and the possible protective effect of probiotics. Methods: 50 healthy albino adult male rats were divided into five equivalent groups. Control group, probiotic group was given 100 μL of suspension containing 1x107 (CFU) of probiotic cocktail daily for 9 days, 5-FU group was received 50 mg/kg of 5-FU by intraperitoneal (IP) injection once daily for 5 consecutive days, probiotic plus 5-FU group was given 50 mg/kg of 5-FU by IP injection for 5 consecutive days with probiotic cocktail once daily for 9 consecutive days and recovery group was received 50 mg/kg 5-FU by IP injection once daily for 5 consecutive days then left without medication till rats had been sacrificed on 9th day .The intestinal tissues have been prepared for a light microscopic study. Results: Rats of 5-FU group showed broadening, fusion and sloughing of villi into lumen, ulcerations, inflammatory infiltration, marked depletion of goblet cells, strong iNOS, marked caspase 3 and weak Ki-67 immuno-expressions. Rats treated with 5-FU plus probiotic showed preservation of normal intestinal architecture with improvement of histological and immune-histological features of mucositis. Rats of recovery group showed decrease histological and immune-histochemical features of mucositis. Conclusion: oral intake of the probiotic could protect against 5-FU induced intestinal mucositis in a rat model.