We prospectively evaluated risk factors for early-onset neonatal (EON) sepsis in a case-control study among inborn patients at the Aga Khan University Medical Centre in Karachi between 1990-1993. A total of 38 cases with blood culture proven bacterial sepsis were identified within 72 hr of birth (prevalence 5.6 of 1000 live births) and matched with two consecutive gender matched births with no complications. The most common isolates were Staphylococcus aureus (18%), group B Streptococci (13%), and Klebsiella pneumoniae (13%). Univariate analysis of maternal risk factors revealed a significant association between maternal urinary tract infection (UTI) (odds ratio [OR]20, 95% confidence interval [CI]2.4-166.9), maternal pyrexia (P < 0.0001), vaginal discharge (P < 0.05), vaginal examinations during labor (P = 0.03), and EON sepsis. The infected newborns also had significantly lower apgar scores at birth (P < 0.0001) and a significantly greater number were intubated at birth (Fisher's exact test P = 0.04). Infected newborn infants were transferred out of the labor room earlier than noninfected controls and significantly fewer received exclusive breastfeeds (OR 0.33, 95% CI 0.1-0.8). Our data suggest the possibility that both vertical transmission from the mother as well as postnatal acquisition of infection from the environment may be of importance in the pathogenesis of EON sepsis in Karachi. Preventive measures should focus at recognition of high-risk infants, strict asepsis during labor, and early institution of exclusive breastfeeding.