Tomatoes act as prebiotics in the gut. The effects of cherry tomatoes on gastrointestinal health have not yet been studied. Four cherry tomato supplementation diets (CTSDs) were prepared from the juice and cake of fresh and processed (heat-treated) cherry tomatoes. The contents of the gut and histological changes in the cecum and intestine were analyzed at 4weeks in rats fed CTSDs. The lactic acid bacteria level in fecal contents of rats fed CTSDs increased compared with the control. The gut length was longer in rats fed CTSDs than that in control animals. In addition, the cecal propionate level significantly increased (p<0.05), and acetate and butyrate levels decreased compared with control animals, however, regardless of the type of CTSD, the total concentration of short chain fatty acids (SCFAs) in all rats fed different CTSDs was similar with the control. The thicknesses of the mucosa and muscle of the cecum and colon increased in rats fed CTSDs compared with the control. CTSDs increased the area of the mucosa and the number of muscle layers in the intestine and cecum of rats, which strengthened the barrier function and promoted gastrointestinal health.