Objectives: The aim of this study was the analysis of conjunctival flora in newborns within the first 72 hours of life, depending on the methods of delivery and other perinatal factors. Material and methods: The study group consisted of 192 mothers and 192 newborns. Culture samples were obtained before delivery from the cervicovaginal secretions of pregnant women and, in case of caesarean sections, additionally from the maternal surface of the fetal membranes. Conjunctival specimens were obtained twice from the inferior conjunctival fornix of the right eye in all the newborns: early sample – immediately after the delivery, and late sample - on the third day of neonatal life. Perinatal factors influencing bacterial colonization were analyzed. Results: Statistically significant difference between the four clinical subgroups was found in the interval between the rupture of the membranes and delivery, number of obstetrical examinations during delivery, antibiotic use during the perinatal period and the presence of green amniotic fluid. Statistically significant difference was observed in the incidence of early sterile samples and method of delivery. The correlation between bacterial species obtained from conjunctival and cervicovaginal secretions samples was also found. The tendency for more frequent occurrence of early sterile samples was observed in newborns of mothers who received antibiotics in the perinatal period and if the interval between the rupture of the membranes and labor was shorter. Conclusions: The obtained data expanded the knowledge about neonatal conjunctival bacterial flora and demonstrated influence of the perinatal factors on bacterial colonization of the infants’ conjunctiva.