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Background: Despite increasing antimicrobial resistance globally, data are lacking on prevalence and factors associated with Staphylococcus aureus (SA) and MRSA carriage in resource-limited settings.Objectives: To determine the prevalence of SA and MRSA nasal carriage and factors associated with carriage among Ugandan regional referral hospital patients.Methods: We enrolled a cross-section of 500 adults, sampling anterior nares for SA and MRSA carriage using Cepheid Xpert SA Nasal Complete.Results: Mean age was 37 years; 321 (64%) were female and 166 (33%) were HIV infected. Overall, 316 (63%) reported risk factors for invasive SA infection; 368 (74%) reported current antibiotic use. SA was detected in 29% and MRSA in 2.8%. MRSA and MSSA carriers were less likely than SA non-carriers to be female (50% and 56% versus 68%, P = 0.03) or to have recently used β-lactam antibiotics (43% and 65% versus 73%, P = 0.01). MRSA carriers were more likely to have open wounds than MSSA carriers and SA non-carriers (71% versus 27% and 40%, P = 0.001) and contact with pigs (21% versus 2% and 6%, P = 0.008). MRSA carriage ranged from 0% of HIV clinic participants to 8% of inpatient surgical ward participants (P = 0.01). In multivariable logistic regression analysis, male sex was independently associated with SA carriage (OR 1.68, 95% CI 1.12–2.53, P = 0.01) and recent β-lactam antibiotic use was associated with reduced odds of SA carriage (OR 0.61, 95% CI 0.38–0.97, P = 0.04).Conclusions: MRSA nasal carriage prevalence was low and associated with pig contact, open wounds and surgical ward admission, but not with HIV infection.