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Background: Non-AIDS-related mortality rates among HIV-infected patients still exceed those of their uninfected peers. A major driver of this excess mortality is a higher risk of non-infectious comorbidities, including cardiovascular disease, chronic kidney disease, type 2 diabetes mellitus, osteoporosis and cancer. The prevalence of mental illness and other chronic non-infectious comorbidities is identified as a primary concern of antiretroviral prescribers in Australia. Methods: We conducted a cross-sectional, observational study using data from MedicineInsight, a large-scale Australian primary care database comprising longitudinal data from electronic clinical information systems. The HIV-infected cohort included all men with a recorded diagnosis of HIV. The non-HIV-infected cohort comprised all other men from the same practices. The prevalence and risk of cardiovascular disease, chronic kidney disease, type 2 diabetes mellitus, osteoporosis, cancer, anxiety and depression were compared between the groups. Results: We included 2,406 HIV-infected males and 648,205 males with no record of HIV diagnosis attending primary care in this study. HIV-infected men were less socioeconomically disadvantaged and more urban-dwelling than men in the primary care cohort. We found that HIV-infected men attending primary care in Australia are at increased risk of chronic kidney disease, cancer, osteoporosis, anxiety and depression. There appears to be a risk of premature onset of cardiovascular disease, osteoporosis and cancer among younger HIV-infected patients. There is a high prevalence of anxiety and depression among HIV-infected men. Conclusions: Increased prevalence of non-infectious comorbidities among HIV-infected men has broad implications for the effective management of those with these chronic conditions. Education to raise awareness among both HIV-infected men and their care providers, together with a greater focus on risk reduction, monitoring and preventive care, may be effective strategies in primary healthcare settings to further narrow the gap in health outcomes between people living with HIV and their uninfected counterparts. [ABSTRACT FROM AUTHOR]