Intrauterine intussusception is well known as one of the rare causes of intestinal atresia. Although the polypoid intussusceptum is usually observed at the obstructed end on the distal side, a few cases with the polypoid lesion located apart from the blind end have been reported. To elucidate the etiology of separated polypoid intussusceptum, we reviewed 42 surgical cases of jejunal or ileal atresia over the last 12 years at Kobe Children's Hospital, Kobe, Japan. Of the 42 cases, 11 were intrauterine intussusception. Two of the 11 cases were associated with polypoid intussusceptums separated from the obstructed ends; the intestinal portion between the polypoid intussusceptum and the obstructed end showed a partial two-fold proper muscle wall and a mesenteric structure invaginated between the two walls. Another case showed linear ulcers facing each other on both the intussusceptum and intussuscipiens. Linear ulceration and subsequent fusion of the intussusceptum and intussuscipiens are suggested to be the pathogenesis of the first two cases.