Background: The prevalence of hypogonadism in HIV-infected patients is still a matter of debate as there is no standardized consensual diagnostic method. In addition, the etiology and endocrine/metabolic implications of hypogonadism in this population remain controversial. This study aims to determine the prevalence of testosterone deficiency in a single-site hospital and to evaluate its association with potential risk factors, lipodystrophy, metabolic syndrome, and cardiovascular risk. Methods: This study analyzed 245 HIV-infected men on combined antiretroviral therapy. Patients with low total testosterone (TT) levels (< 2.8 ng/mL) and/or low calculated free testosterone (FT) levels (< 6.5 ng/dL) were considered testosterone deficient. According to their LH and FSH levels, patients were classified as having hypogonadotropic or hypergonadotropic dysfunction. Other clinical, anthropometric, and analytic parameters were also collected and analyzed. Results: The prevalence of testosterone deficiency in our population was 29.4 %. Among them, 56.9 % had hypogonadotropic dysfunction and 43.1 % presented with hypergonadotropic dysfunction. Patients with testosterone deficiency were older (p < 0.001), had higher HbA1c levels (p = 0.016) and higher systolic blood pressure (p = 0.007). Patients with lower testosterone levels had higher prevalence of isolated central fat accumulation (p = 0.015) and had higher median cardiovascular risk at 10 years as measured by the Framingham Risk Score (p = 0.004) and 10-Year ASCVD risk (p = 0.002). Conclusions: The prevalence of testosterone deficiency in this HIV population is high, with hypogonadotropic dysfunction being responsible for the majority of cases. Testosterone deficiency might predispose to, or be involved, in the pathogenesis of HIV-associated lipodystrophy. Patients with low testosterone levels have higher cardiovascular risk, highlighting the importance of early diagnosis of this condition.