Objective: This study aimed to investigate the Epstein-Barr virus (EBV) prevalence and viral load in subgingival sites of human immunodeficiency virus type 1 (HIV-1) positive (HIV+) individuals, correlating subgingival EBV load to the clinical periodontal condition, HIV systemic load, EBV systemic load, and use of antiretroviral therapy (ART). Method and materials: Ninety individuals were recruited and divided into three categories: those without periodontal disease (G1), with gingivitis (G2), and with periodontitis (G3). Subgingival biofilm and blood samples were analyzed by quantitative polymerase chain reactions (qPCR). A questionnaire was administered to collect general information about patients, and data regarding HIV and use of ART were accessed from their medical records. Results: EBV was detected in 85.6% of the samples. Comparing subgingival and systemic load of EBV in G1, G2, and G3, there was a statistical difference only in G3 (3.93 log10 copies/mL and 5.47 log10 copies/mL, respectively; P = .014), where EBV load was higher in periodontal pockets than in the blood. All groups had high EBV loads in subgingival sites (> 2,000 copies/mL). A positive linear correlation between systemic HIV load and EBV subgingival load was found in G1 and G2 (r = 0.647; P .001), but not in G3. Only G1 individuals using ART had lower subgingival EBV loads than those not using it (5.03 log10 copies/mL, and 7.14 log10 copies/mL, respectively; P = .0348). Conclusions: Subgingival sites, especially the periodontal pockets, are suggested to act as a reservoir of EBV in HIV+ individuals. Therefore, the identification of latent EBV infections in this easily accessible site might help to improve quality of life in patients with HIV by maintaining oral/periodontal health. In addition it might encourage new approaches in investigating EBV-associated disorders in HIV+ patients. Keywords: antiretroviral therapy, Epstein-Barr virus (EBV), HIV-1, human herpesvirus-4, periodontal diseases, periodontal pocket