Staphylococcal colonization is a risk factor for healthcare-associated infections, which are frequent in Neonatal Intensive Care Units (NICU). This study analyzed microbiology, epidemiology and clinical aspects of Staphylococcus spp. colonizing neonates. Nasal or periumbilical swabs were evaluated from 175 newborns admitted to a NICU of a Rio de Janeiro hospital from March to September 2009. Clinical data were obtained from the medical records. SCCmec typing and the mecA and Panton-Valentine Leukocidin (PVL) genes were detected by PCR. Clonal diversity was evaluated by pulsed-field gel electrophoresis. Staphylococcus spp. isolates were detected in 98 (56%) neonates, 66.3% of them had birth weight ≤ 2500 g, 62.2% were preterm (˂ 37 weeks) and the mean length of hospitalization was 14.9 days. Among the 133 isolates identified, 48.1% were S. epidermidis, 23.3% S. haemolyticus and 13.5% S. aureus. Methicillin-resistant Staphylococcus isolate was detected in 77.6% of neonates. The methicillin-resistant S. aureus isolates carried the SCCmec type IV, while 94.6% of S. epidermidis and 85.7% of S. haemolyticus presented non-typeable cassettes. Among the S. aureus, 55.6% had PVL genes and the USA800 genotype was prevalent. Two genotypes of S. epidermidis and one of S. haemolyticus clustered 42.2% and 25.8% of the isolates, respectively. S haemolyticus colonization was associated with the use of parenteral nutrition and mechanical ventilation. High rate of neonates colonized by methicillin-resistant Staphylococcus species and the permanence of clones circulating in the NICU highlight the importance for continuous and preventive surveillance in this high-risk population.