We reviewed the medical records of patients diagnosed with neonatal bacterial conjunctivitis with positive cultures of conjunctival secretion. Sociodemographic variables of the mother and the neonate, associated risk factors, results of the microbiological isolations, topical and systemic antibiotic therapy and antibiotic sensitivity were recorded. Results: A total of 69 newborns were identified, 65.22% were male, the average age was 15.7 ± 8.3 days. Major etiological agents identified were Staphylococcus epidermidis (n = 20, 28.9%), Staphylococcus aureus (n = 12, 17.3%) and Haemophilus influenzae (9 patients, 13.0%). There were no positive isolates for Chlamydia trachomatis or Neisseria gonorrhoeae. The most common maternal peripartum risk factors were premature rupture of the ovular membranes (n = 16, 21.33%), urinary tract infection (7 cases, 10.1%), preterm birth syndrome (n = 6, 8.00%) and bacterial vaginosis (5 cases, 7.25%). Resistance to oxacillin 26% (n = 18) and tetracyclines 15% (n = 11) was observed in patients with Staphylococcus infection. Conclusion: Over the years, the epidemiology of neonatal conjunctivitis has changed. Nowadays, gonococcal pathogens are not the most common cause of neonatal conjunctivitis. A significant number of patients with methicillin-resistant S. aureus were observed.