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Objectives: Atherosclerosis has been linked with periodontitis in the general population and with persistent immune activation and a high burden of cytomegalovirus (CMV) in HIV patients responding to antiretroviral therapy (ART). Here, we assess risk factors for cardiovascular changes in younger HIV patients representative of patient populations in Asia., Study Design: HIV-infected adults (n = 82) with <200 CD4 T-cells/μl were examined as they began ART at Cipto Mangunkusumo Hospital, Jakarta, and after 3 months. 32 patients were re-assessed after 5 years, alongside 32 age-matched healthy controls., Methods: We assessed the community periodontal index of treatment needs, carotid -thickness (cIMT), plasma markers of immune activation (using commercial enzyme-linked immunosorbent assay) and CMV antibodies by in-house enzyme-linked immunosorbent assay., Results: Periodontitis persisted in 16/32 patients after 5 years and was potentiated by greater age (P = 0.03) and poor oral hygiene (P = 0.05), with no effect of smoking, pulmonary tuberculosis, oral candidiasis, or low CD4 T-cell counts (P > 0.05). After 5 years on ART, right and left cIMT were greater in HIV patients with periodontitis (P = 0.02, 0.006, respectively). Moreover, cIMT values were higher in patients with periodontitis (P = 0.05-0.01) than in equivalent controls. Simple linear regressions showed that patients with periodontitis had greater right (P = 0.01) and left (P = 0.004) cIMT than those without periodontitis. Multiple linear regressions showed that periodontitis and CMV antibody levels optimally predicted poor right and left cIMT (Adjusted R = 0.36, P = 0.0013; Adjusted R = 0.40, P = 0.001, respectively)., Conclusions: Our data identify periodontitis and CMV as independent predictors of atherosclerosis in young adult HIV patients.