Necrotizing enterocolitis is a severe inflammatory disease in premature infants that is characterized by wounds in the intestinal wall. The ongoing dynamics of the disease depend upon a complex interplay between the immune system, intestinal bacteria, and intestinal epithelium. We have developed a three-dimensional computational model that examines this complex interplay and its dependence on the spatial structure of the intestine. The model reproduces expected physiological results and shows that the spatial structure of intestinal wounds may affect the outcome of necrotizing enterocolitis.