Neonatal sepsis remains a major cause of morbidity and mortality in the neonatal period. The aim of this study, was to detect the source of infection in early onset neonatal sepsis. This study was carried out on 352 mothers who came to delivery in Kasr-El-Aini Hospital and their newborns in the period between March 2002 and February 2003. Swabs were taken from skin of babies (from nostril, axilla, umbilicus, groin and anus), vagina and cervix of the mothers and different environmental substances. Microbiological examination of all swabs were done. Also, blood cultures were done for septic neonates. The enrolled neonates were classified into 2 groups : septic group (87 neonates) and non-septic group (265 neonates). Blood cultures were positive in 79 neonates. Coagulase-negative staphylococcus was the most common organism isolated from the surface of the neonates and from blood cultures. We found that colonization of the skin of newborn with virulent organisms can occur through transmission from maternal genital tract during delivery. Colonization of baby’s skin especially umbilicus and groin is a portal of invasive infection in the neonate. Also, contamination of material and equipment used for mothers and their babies during delivery is an important source of pathogens causing neonatal infection.