Background: Neonatal morbidity and mortality are major public health challenges in our local environment with a huge percentage of deaths in the neonatal period attributable to sepsis. Aim: The aim of the study was to assess the factors that affect patientsâ€™ outcome with respect to sepsis in neonates. Methods: This was a prospective descriptive cross sectional study. Neonates with proven and suspected sepsis were recruited into the study. Outcome was assessed based on the length of hospital stay and mortality. Clinical response to treatment was also assessed. Results: Nine factors were identified as risk factors for mortality, birth weight (< 2500g P = 0.000, OR = 7.214, CI = 2.5 â€“ 21.0), prolonged rupture of membranes (PROM) (P = 0.014, OR = 2.470, 95% CI = 1.2 -5.1), prolonged preterm rupture of membranes (PPROM) P = (0.046. OR = 2.1, 95% CI = 0.9 -4.6) multiple gestation (P = 0.009), an infectious clinical diagnosis (P = 0.046, OR = 0.480), frequent changes in antibiotics (P = 0.013). Others were a low Apgar score (P = 0.000), presence of organisms in intravenous fluids (P = 0.042, OR = 0.2, 95% CI = 0.02 â€“ 1.3 and the presence of organisms in the blood stream (P = 0.007). Conclusion: This study determined the mortality rate in our environment due to sepsis to be 15.7%. Risk factors for a poor outcome include low birth weight, perinatal period, and maternal illness in pregnancy and isolation of a pathogen from the blood stream.