HIV-positive individuals are at higher risk of Methicillin Resistant Staphylococcus aureus (MRSA) colonization and its related infection. There is limited data in the nation on the prevalence and risk factors of MRSA colonization among HIV patients. The aim of this study was to address the existing knowledge gap. Cross sectional study was carried out from September 2014 to February 2015 in three selected health centers and one general hospital. A standardized questionnaire was developed for collection of socio-demographic and clinical data. A total of 498 Nasal and throat swabs (two for each patient) were collected from 249 patients, transported and processed using standard bacteriological procedures. Data was analyzed using Chi square (X2) test and associated risk factors were determined. P < 0.05 was considered statistically significant. Out of 249 study participants, S. aureus was isolated from 81 (32.5 %) patients, with MRSA colonization rate of 6 (2.4 %). MRSA isolates were resistant to Ciprofloxacin and trimethoprim-sulphamethoxazole (16.7 % each), clindamycin (33.3 %) and erythromycin (50 %). However, all MRSA isolates were 100 % sensitive to Amikacin. History of hospitalization, percutaneous device usage, patients with a household member’s hospitalization and low CD4 count (<200 cells/mm3) were significantly associated with S. aureus colonization (p < 0.05).