The main objective of this study is to determine neonatal sepsis among neonates born to Chlamydia trachomatis (CT) infected mothers. One hundred and one neonatesborn to CT infected mothers were screened for CT infection by polymerase chain reaction (PCR).Maternal and neonatal risk factors for sepsis were also assessed using a checklist. Thirty-four of the neonates had sepsis of these, twenty-two(22) were early onset and 12 late onset. Neonatal infections included respiratory tract infections (RTI) 16; blood stream infection (BSI) 7; gastrointestinal tract (GIT) infections 5; urinary tract infection (UTI) 3; conjunctivitis (CONJ) 2; otitis media (OM) 1. Premature rapture of membrane (PROM) p<0.001); foul smelling liquor (FSL, p<0.001) intra partum fever (IPF) p<0.001) and meconium stained amniotic fluid (MSAF) p<0.001) were maternal factors found to have significantly increased the risk for CT infection in the neonate.Preterm birth (p<0.00O1) low birth weight and APGAR score less than 7 were neonatal characteristics found to have increased the risk for CT associated sepsis in the neonate.Caesarian section significantly reduced the risk for vertical transmission of CT (p<0.05).Routine screening and treatment of pregnant women for CT infection is recommended to reduce neonatal morbidity and mortality.