OBJECTIVE To investigate bacterial associations of S. pneumoniae, S. aureus, and H. influenzae in the nasopharynx of ambulatory children with HIV infection. METHODS A cross-sectional nasopharyngeal swab survey of 148 children with HIV infection from West Bengal presenting for routine outpatient care was conducted. RESULTS Forty-one (28 %) children carried S. pneumoniae, 35 (24 %) carried S. aureus and 39 (26 %) carried H. influenzae. Seventeen (11 %) had dual colonization with S. pneumoniae and H. influenzae, 13(8.8 %) had dual colonization with S. pneumoniae and S. aureus, and 6(4 %) had dual colonization with S. aureus and H. influenzae. Three (2 %) had triple carriage with H. influenzae, S. aureus, and S. pneumoniae. Neither Cotrimoxazole prophylaxis nor ART (antiretroviral therapy) affected colonization with any organism. There was no association between HIV immune status, recent antibiotic use, exposure to other children, household tuberculosis exposure and colonization with any organism. There was a strong negative association between malnutrition and colonization with H. influenzae. CONCLUSIONS The negative association between S. pneumoniae and S. aureus colonization in the nasopharynx described in healthy populations was not present. The authors found a strong positive association between carriage with H. influenzae and S. pneumoniae. These findings provide insight into the increased risk of invasive disease from these organisms in HIV infected children.