OBJECTIVE To determine nasopharyngeal colonization rates of two vaccine preventable bacterial pathogens Hemophilus influenzae type b (Hib), and Streptococcus pneumoniae (Pneumococcus), antibiotic susceptibility of isolates, factors associated with their colonization, and immunization history in a cohort of HIV infected children. METHODS The authors conducted a cross-sectional nasopharyngeal swab survey of 151 children affected with HIV presenting for routine outpatient care in West Bengal, India. RESULTS 151 HIV affected children were enrolled. The median age was 6, 148/151 children were HIV positive, 65% had moderate to severe malnutrition, 53% were moderately to severely immunosuppressed, 17% were on antiretroviral therapy (ART), 90% were on cotrimoxazole prophylaxis (TMP/SMX). None had received the pneumococcal or Hib conjugate vaccines. Hib prevalence was 13% and pneumococcal prevalence was 28%. Children with normal or moderate immune suppression had high rates of colonization compared to those with severe immunosuppression (71% Hib, 61% pneumococcus). Hib and pneumococcal isolates had high rates of resistance to tested antibiotics including TMP/SMX and third generation cephalosporins. Neither ART nor TMP/SMX prevented colonization. Children colonized with multidrug resistant isolates had high rates of exposure to TMP/SMX. CONCLUSIONS HIV infection, late access to ART, high rates of colonization to resistant organisms and lack of access to vaccines makes this population vulnerable to invasive disease from Hib and pneumococcus.