This study examined the effects of milk protein pre-hydrolyzation on the crypt cell proliferation and morphological alterations in the small intestine in neonatal piglets. The newborn unsuckled Erhualian piglets were bottle-fed for 3 days with cow milk formula or pre-hydrolyzed cow milk formula. When compared with newborn pigs, the height of the intestinal villi decreased by 30-45% in jejunal region inmilk-fed piglets, while no significant change was observed in the intestinal villus height in piglets fed pre-hydrolyzed milk. Microscopic examination showed an atrophy of the intestinal villi and accelerated proliferation of crypt cells in the milk-fed piglets, possibly due to a hypersensitive reaction of the intestine to dietary protein. The results indicate that the nature of dietary protein had a significant effect on the intestinal structure. This finding may have a significant implication in infant care and animal feeding.