An important indicator to recommend a protein source for piglet nutrition is the absence of intestinal damage. The effects of sesame or soybean meal based diets on Gastrointestinal Tract (GIT) morphophysiology, diarrhea incidence and severity in piglets were studied during the first two weeks postweaning. Thirty-six piglets weaned at 21 days of age were fed one of three diets: A control casein diet (C), a Sesame Meal diet (SM), or a Soybean Meal Diet (SBM). Diarrhea incidence and fecal score were determined once daily over a 14-day period. After 14 days, 3 piglets in each experimental group were fasted 12 h, fed for 1 hour and then slaughtered at 3, 6, 9 and 12 h after feeding, at which times relative GIT weights (g·kg −1 ), intestinal morphology, digesta pH, trypsin and chymotrypsin activities were evaluated.Stomach and small intestine weight were higher (p<0.05) in piglets fed SBM and SM than in piglets fed C. The gastric pH was higher in piglets fed C and SM and lower in piglets fed SBM (p<0.05). The pH of the different segments of the GIT was not affected (p>0.05) by dietary protein source. The specific activity of chymotrypsin was higher (p<0.05) in animals fed C than in those fed SM and SBM and did not vary with after feeding time (p>0.05). Trypsin activity was higher (p<0.05) in piglets fed SBM than those fed C and SM. The dietary protein source had no impact (p<0.05) on villus height or duodenal and ileal crypt depth. Jejunal villi in piglets fed SBM were shorter (p<0.05) than in piglets fed C and SM. Dietary treatment had no effect on diarrhea incidence and severity. These findings show that sesame meal can replace soybean meal as a protein source in starter diets for weaned piglets.