Background: Antimicrobial resistance (AMR) is a growing public health threat around the world and is not well characterized in the developing setting. Specifically, there is a lack of information regarding nasal colonization with S. aureus and methicillin-resistant Staphylococcus aureus (MRSA) in Latin America and Peru. Methods: This is the report of the baseline findings of a prospective cohort study followed up over 1 year at four geographically and ecologically distinct Peruvian Air Force bases in order to determine S. aureus nasal colonization prevalence and risk factors. Additionally, all MRSA isolates underwent molecular analysis which included pulsed-field gel electrophoresis and determination of virulence and resistance genes. Results: We enrolled 756 military personnel. Anterior nares colonization with Staphylococcus aureus was detected in 73 of 756 participants (9.7 %) and MRSA was detected in 2 of 756 (0.3 %). Colonization rates differed significantly (P = 0.02) between geographic enrollment sites: Talara-4.3 %, Iquitos-9.1 %, Arequipa-14.0 % and Lima-11.3 %. Risk factors for S. aureus colonization included being male and a reported history of respiratory disease. Conclusion: Overall, we found low prevalence of S. aureus and MRSA nasal colonization in this Peruvian military population. These findings contribute to the overall epidemiological understanding of S. aureus and MRSA in Latin America. The colonization rates which varied based on geographical location warrants further study.