Neonatal conjunctivitis is one of the most important consultation reasons in the first days of life. Causes may be chemical or infectious. Neonatal conjunctivitis study for common microorganisms and Chlamydia trachomatis is being performed at Posadas Hospital since 1995, in a progressive form. The objective of this study was to know the epidemiological situation in the last five years (1999-2003), and to describe the variations detected between two periods, 1995-1998, and 1999-2003. It was observed no change about C. trachomatis prevalence (8%), during all the time in the population studied. With regard to common microorganisms it was showed a decrease in the second period (36.6%) with respect to the first (52.4%). Likely, the causes may be due to changes about sample collection conditions, or to epidemiological variations. The most frequent microorganisms found were: Staphylococcus aureus 69 (27.6%), Streptococcus pneumoniae 68 (27.2%), and Haemophilus influenzae 64 (25.6%). We consider important to evaluate the kind of ocular secretions at the first consultation, which can lead to a symptomatic treatment that will be corroborated or not, according to microbiological results.