The aim of this short communication is to assess colonization by MRSA, penicillin-resistant pneumococci (PRP), fluconazole-resistant (FLU-R) Candida albicans (CA) and non-albicans Candida (NAC), and ciprofloxacin-resistant E. coli with regard to immune recovery due to CD4 T-cell increase depending on the duration of highly active antiretroviral therapy (HAART). Prior exposure to oral cephalosporins (P<0.01) was significantly related to MRSA colonization. Penicillin-resistant pneumococci were more frequently (40% vs. 12.5%, NS) related to prior cephalosporins, but not to penicillins or macrolides use. However, this association was not statistically significant. Prior receiving of fluconazole was also not associated with increased colonization by FLU-R Candida spp. (30% vs. 16.7%, NS). Cotrimoxazole (P<0.01) and amoxicillin/amoxicillin clavulanate (P<0.01) were surprisingly protective against colonization by fluconazole-resistant Candida spp. Exposure to quinolones was not a risk factor for colonization by ciprofloxacin-resistant E. coli, but receiving of rifampin was (P<0.01). Colonization by cefotaxime-resistant Klebsiella spp. and Enterobacter spp. was not significantly associated with cephalosporins, but it was with cotrimoxazole use (P<0.05). In addition, HIV-infected children on HAART who received any antibiotic were significantly more colonized by cotrimoxazole-resistant E. coli (P<0.01) than those not receiving any antibiotic prior to colonization. Exposure to cephalosporins and macrolides was significantly related to cotrimoxazole-resistant E. coli (100% vs. 20%, 75% vs. 10%; P<0.01 for both), but exposure to cotrimoxazole itself was not.