We collected all Staphylococcus aureus isolates from the National Children's Hospital in Costa Rica to evaluate the prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). Of 299 S. aureus isolates, 61% were MRSA. Most MRSA isolates (94.5%) carried SCCmec IV, and 45.6% carried Panton-Valentine leukocidin-encoding genes. The high prevalence of MRSA in this population highlights the need for improvement of antibiotic prescription and infection control measures.