OBJECTIVES:To study the effect of short‐chain fatty‐acids on atrophy and inflammation of excluded colonic segments before and after the development of diversion colitis.INTRODUCTION:Diversion colitis is a chronic inflammatory process affecting the dysfunctional colon, possibly evolving with mucous and blood discharge. The most favored hypotheses to explain its development is short‐chain fatty‐acid deficiency in the colon lumen.METHODS:Wistar rats were submitted to colostomy with distal colon exclusion. Two control groups (A1 and B1) received rectally administered physiological saline, whereas two experimental groups (A2 and B2) received rectally administered short‐chain fatty‐acids. The A groups were prophylactically treated (5th to 40th days postoperatively), whereas the B groups were therapeutically treated (after post‐operative day 40). The mucosal thickness of the excluded colon was measured histologically. The inflammatory reaction of the mucosal lamina propria and the lymphoid tissue response were quantified through established scores.RESULTS:There was a significant thickness recovery of the colonic mucosa in group B2 animals (p  =  0.0001), which also exhibited a significant reduction in the number of eosinophilic polymorphonuclear cells in the lamina propria (p  =  0.0126) and in the intestinal lumen (p  =  0.0256). Group A2 showed no mucosal thickness recovery and significant increases in the numbers of lymphocytes (p  =  0.0006) and eosinophilic polymorphonuclear cells in the lamina propria of the mucosa (p  =  0.0022).CONCLUSION:Therapeutic use of short‐chain fatty‐acids significantly reduced eosinophilic polymorphonuclear cell numbers in the intestinal wall and in the colonic lumen; it also reversed the atrophy of the colonic mucosa. Prophylactic use did not impede the development of mucosal atrophy.