This study investigated the association of IL-1A (+4845) and IL-1B (+3954) gene polymorphism with the subgingival microbiota and periodontal status of HIV-infected Brazilian individuals on highly active antiretroviral therapy (HAART). One hundred and five subjects were included in the study, distributed into 2 HIV groups [29 chronic periodontitis (CP+) and 30 periodontally healthy (H+)]; and 2 non-HIV groups (29 CP- and 17 H- patients). IL-1A and B were genotyped by PCR and restriction enzyme digestion. Thirty-three bacterial species were detected by checkerboard. Overall, we observed a prevalence of the allele 2 in the IL1-A and IL-1B polymorphism at 30.5% and 25.7%, respectively. Only 11.4% of all patients were composite genotype-positive, and 75% of those were HIV-infected. No significant associations between polymorphism of the IL-1 gene and periodontitis or HIV infection were observed. Likewise, no significant differences in the frequency and counts of any bacterial species were found between individuals with and without allele 2 (IL-1A or IL-1B). The data indicated that the IL-1 gene polymorphism is neither associated with periodontal destruction nor with high levels of subgingival species, including putative periodontal pathogens in HIV Brazilian individuals on HAART.