To compare the nutrient digestibility of soybean meal (SM) and pigeon pea seed meal (PM) as well as morphological intestinal alterations in piglets fed them, three pigs per group were randomly selected at the end of the feeding experiment for ten days. Growth performance was higher in the SM group than in the PM group (p<0.05). The digestibility of crude protein, crude fat and crude fiber was 80.6%, 23.6% and 52.4% in the SM group, while in the PM group, values of 49.8%, 23.6% and 43.2% were observed, respectively. Digestible energy was 3.26 kcal g^-1 in SM and 3.17 kcal g^-1 in PM. It was concluded that the digestibility of PM was lower than that of SM; almost half of the protein in PM was digested. Dietary treatments had no effect on length of each small intestinal segment and weight of visceral organs (small intestine, liver, heart, spleen, kidney, stomach and lung) except the decreased kidney weight in the PM group (p<0.05). The epithelial cells on the jejunal villi showed a dome-like shape in the SM group, but they were a flat shape in the PM group. The present digestion trial and histological intestinal data suggest that the intestinal digestive and absorptive functions are much more atrophied in the PM group than in the SM group, and demonstrate that histological intestinal alterations might be well related with the intestinal functions.