The emergence of Community-associated methicillin-resistantStaphylococcus aureus(CA-MRSA) infections among indigenous populations has been reported. Usually, indigenous communities live in extreme poverty and are at risk of acquiring infections. In Brazil, healthcare inequality is observed in this population. To date, there are no reports of CA-MRSA infections, and no active search for asymptomaticS. aureuscarriage has been conducted among Brazilian Indians. The aim of this study was to investigate the prevalence of colonization withS. aureusand CA-MRSA among Brazilian Indians. We screened 400 Indians (from near urban areas and remote hamlets) forS. aureusand CA-MRSA colonization. The isolates were submitted to clonal profiling by pulsed-field gel electrophoresis (PFGE), and selected isolates were submitted to multilocus sequence typing (MLST). Among 931 specimens (nasal and oral) from different indigenous individuals in remote hamlets,S. aureuswas cultured in 190 (47.6%). Furthermore, CA-MRSA was found in three isolates (0.7%), all SCCmectype IV. PFGE analysis identified 21 clusters among theS. aureusisolates, and MLST analysis showed a predominance of sequence type 5 among these isolates. Our study revealed a higher prevalence ofS. aureuscarriage among Shanenawa ethnicity individuals (41.1%). Therefore, ethnicity appears to be associated with the prevalence ofS. aureusin these populations.