Congenital atresias of the gastrointestinal tract are usually single and divided into three forms on a morphologic basis. The septal or diaphragmatic type (type I) is the least common. We report an infant with multiple type I atresias involving both the small and large intestine and describe the unique histologic features of the septa: fragmentation of muscularis mucosa, multiple septal cysts lined by columnar epithelium, circular and longitudinal muscular layers, and absence of inflammation. This infant had a sibling who died with multiple intestinal atresias of the septal type. The histologic features suggest that type I gastrointestinal atresias may be due to failure of complete recanalization rather than result from healing of vascular of inflammatory events.