In Japan, mortality due to intestinal perforation has been increasing for the last 15 years, as the survival rate of extremely-low-birth-weight neonates (ELBWs) has been increasing. In our NICU, although the incidence of necrotizing enterocolitis has been decreasing, that of focal intestinal perforation (FIP) has been increasing. To elucidate the pathogenesis of FIP, a histological study was performed. For the last 20 years, in our NICU, 11 ELBWs with FIP, including one with multiple perforations and impending rupture, underwent laparotomy and enterostomy. The intestinal wall around the perforation was resected for histological study. Histological studies revealed well-developed ganglion cells in all the cases. Although some lymphocytic infiltration and hemorrhage were observed, no apparent neutrophilic infiltration, or necrotic change was identified in any case. No evidence of microcirculatory impairment was identified. The intestinal musculature discontinued abruptly with thinning in three cases, and without thinning in the others. The histology of impending rupture showed an absence of the muscularis with preservation of the remaining components of the bowel wall. The findings that the punched-out perforations had the appearance of Hirschsprung's disease, FIP exclusively occurred in ELBWs, and that neither mechanical obstruction nor necrotic change could be identified as the cause of the perforation suggest that immature bowel movement and congenital muscle defects may be involved in the pathogenesis of FIP.