Background: Gastrointestinal perforation in the newborn is common, and often associated with poor outcome in developing countries. We determined the etiology and outcome of neonatal gastrointestinal perforation in an underserved region. Methods: A prospective study of neonates who presented with gastrointestinal perforation at the University of Benin Teaching Hospital, Benin City, and Leadeks Medical Center, both in Edo state, Nigeria, between July 2001 and June 2008. Results: A total of 68 neonates aged between 1 and 28 days (mean 12 ± 2.1 days), weighing from 1.5 to 4.1 kg (mean 2.8 ± 1.3kg), and comprising 41 males and 27 females (ratio 1.5:1) presented with gastrointestinal perforation. Fifty-one (75%) neonates had perinatal distress, following complicated delivery in 47 (69.1%) and drugs/infections in 4 (5.9%). These factors were the only cause of perforation (primary perforation) in 21 (37.5%) neonates, increased the risk of perforation of gut pathologies (secondary perforation) in 30 (62.5%), while only 17 (25%) neonates with perforation had no perinatal distress. Emergency caesarean delivery, prolonged rupture of membrane, prematurity, pre-partum hemorrhage, drugs, infections and maternal diabetes mellitus were the causes of perinatal distress. Volvulus. 20 (29.4%) anorectal anomaly, 14 (20.6%) necrotizing entero colitis, 11 (16.2%) and Hirschsprung’s disease, 2 (2.9%) were causes of secondary perforations. Late presentation of clinically compromised neonates was frequent with attendant 27 (39.7%) deaths. Conclusions: Factors associated with perinatal distress were the leading causes of gastrointestinal perforation in neonates. The mortality was high and antenatal care in hospitals with adequately supervised delivery and early referrals are advocated to improve outcome.Keywords: Neonates, gastrointestinal perforation, perinatal distress.