One hundred and fifty five neonates with conjunctivitis admitted into the neonatal unit at the Lagos University Teaching Hospital were microbiologically investigated. This was to determine the bacterial aetiologic agent(s) in neonatal eye infection and highlight some risk factors. Antimicrobial susceptibility testing was done on the pathogens isolated using the diskagar diffusion method. The incidence of conjuctivitis in the newborn was 18 per 1000 live births. Predisposing factor noted were vaginal delivery, asphyxia neonatorum and prolonged rupture of membrane. Pathogens predominantly isolated were Staphylococcus aureus (37.4%), Coagilase negative Staphylococci (12.3%), Klebsiella pneumoniae (12.9%) and Pseudomonas aeruginosa (8.2%). Antimicrobial suscepibility results revealed varied degrees of susceptibility to ofloxacin (75%), Cloxacillin, erythromycin, Gentamicin and augumentin (30%) by the gram positive bacteria while most of the gram negative were susceptible to colistin and ofloxacin (above 90%). The high incidence of bacterial eye infection should be minimized by the elimination of the risk factors and adoption of stringent aseptic measures in the care of the neonate.