BackgroundBabies born via caesarean section in low-income settings face a higher risk of early-onset neonatal sepsis (EONS), which has greater mortality than late-onset sepsis. However, maternal factors contributing to EONS among caesarean-delivered babies in these settings, including Uganda, are not well documented. We determined maternal factors associated with EONS among term babies delivered by caesarian section at Mbarara Regional Referral Hospital (MRRH), southwestern Uganda.MethodsWe conducted an unmatched case-control study at MRRH from December 2019 to March 2020. Cases were caesarean section-delivered term babies with EONS (within 72 h). Controls were caesarean section-delivered term babies without EONS. We enrolled mother-baby pairs for both groups, obtaining maternal data via structured questionnaires The diagnosis of EONS was made using the WHO Young Infant Integrated Management of Childhood Illnesses algorithm. Cases were consecutively recruited while controls were recruited by simple random sampling in a ratio of 1:2. We excluded newborns whose mothers were too ill to consent. We used multivariable logistic regression analysis to identify maternal factors associated with EONS.ResultsWe enrolled 52 cases and 104 controls. The mean age for the mothers was 27 (± 5.5) years. Neonates born to referred mothers had higher odds of EONS than those born to non-referred mothers (AOR = 6.2, 95% CI: 1.8–21). Additionally, decision-to-delivery time > 1 h for emergency caesarean section (AOR = 16, 95% CI: 4.2–65), antepartum hemorrhage (AOR = 8.0, 95% CI: 1.6–40), primiparity (AOR = 4.8, 95% CI: 1.1–21), and > 3 vaginal examinations after membrane rupture (AOR = 4.3, 95% CI: 1.5–12) were associated with EONS.ConclusionsPrime gravidity, antepartum hemorrhage, multiple vaginal examinations after membrane rupture, long decision-to-delivery time, and referral status were associated with EONS among term babies delivered by caesarean section at MRRH. To reduce EONS risk, clinicians should limit post-membrane rupture vaginal exams or consider prophylactic antibiotics if multiple exams are needed. Screening babies born to primiparous women, those referred, those with antepartum hemorrhage, multiple vaginal exams after membranes rupture, and long decision-to-delivery times, could aid prompt recognition of EONS and timely interventions. Implementing standard procedures to reduce caesarean decision-to-delivery time could reduce risk for EONS in this setting.