Malabsorption syndrome (MAS) in broilers is characterized by enteritis and reduced body weight gain. The pathogenesis of the intestinal lesions and the reasons for susceptibility differences between broiler lines are not clear. We studied the development of enteric lesions, epithelial apoptosis, and cell proliferation in relation to susceptibility. One-day-old chickens from two broiler lines were orally inoculated with intestinal homogenate derived from MAS-affected chickens. Vacuolar degeneration and apoptosis of the villous epithelium and infiltration of heterophils into the lamina propria occurred from day 1 post-inoculation. Following heterophil accumulation, at day 4 to 6 post-inoculation, there was severe apoptosis of the crypt epithelium and villous atrophy. The susceptible broilers had a significantly greater influx of heterophils and, subsequently, severe epithelial apoptosis and cystic damage to the crypts. There appeared to be a causal relationship between heterophil influx and the onset of apoptosis. Coincident with the epithelial apoptosis, MAS-affected chickens had crypt hyperproliferation and faster epithelial turnover. Heterophil infiltration and epithelial apoptosis appear to be critical in the pathogenesis of MAS. Heterophil recruitment may be a major factor in differences in susceptibility to MAS.