Infants, especially extremely low birth weight infants (ELBWIs, birth weight <1,000 g) continue to have a high mortality after gastrointestinal (GI) perforation. In Japan, the overall mortality rate for neonates under 30 days having GI perforation was 31.6% in 2003. From 1974 to 2003, 34 cases of GI perforation in neonates were treated surgically in Fukuoka University Hospital. The overall mortality rate was 50% (17 of 34). Etiologies included necrotizing enterocolitis (NEC) (35.3%), meconium peritonitis (25%), idiopathic (25%), and gastric perforation (11.8%). The present series was divided into four groups: survival and non-survival neonates of the early (1974 to 1997) and recent (1998 to 2004) periods. Several prognostic factors of neonatal GI perforation were compared between several groups. The gestational week (GW) at birth, birth weight (BW) and weight at operation were significantly lower for non-surviving neonates in the recent period compared with the other three groups. Although a real improvement in surgical outcome was noted with improved neonatal intensive care management, the mortality rate was still high, especially in extremely premature cases under both 1,000 g and 29 GWs. The vast majority of these extremely premature babies thus comprised the NEC patients. It is therefore necessary to substantially improve the medical treatment level for such premature babies.