PURPOSE: This study was conducted to compare the clinical features and outcome of neonatal gastrointestinal perforation due to necrotizing enterocolitis (NEC) and other etiologic diseases (non-NEC). METHODS: The medical records of neonates, admitted to the neonatal intensive care unit of Dongsan Medical Center for gastrointestinal perforation between January 1999 and December 2009, were reviewed retrospectively. The admission records for clinical findings and mortality were reviewed and statistically analyzed for both groups. RESULTS: Among 28 neonates, NEC group was 35.7% and the other group (intestinal atresia, malrotation, meconium peritonitis, etc) was 64.3%. The mean gestational age was significantly shorter (32.8+/-4.6 weeks vs. 36.8+/-2.7 weeks, P=0.028) and the mean diagnostic day was significantly later (16.3+/-9.7 days vs. 2.2+/-1.8 days, P=0.001) in the NEC group than that of the non-NEC group. The mortality rate was markedly higher in the NEC group (50%) than that of the non-NEC group (5.6%)(P=0.013). By simple logistic regression analysis, gestational age (OR 0.69, 95% CI: 0.51-0.95, P=0.022) and NEC (OR 17.00, 95% CI: 1.60-181.36, P=0.019) were the significant risk factors to increase the mortality rate. Multiple logistic regression analysis showed NEC (OR 7.70, 95% CI: 0.55-108.06, P=0.130) and gestational age (OR 0.79, 95% CI: 0.58-1.09, P=0.151) were not the significant independent risk factors. CONCLUSIONS: This study found that gestational age was shorter and mortality rate was higher in the NEC group than the non-NEC group. However, after multiple logistic regression analysis, NEC or lower gestational age itself did not increase the mortality rate significantly.