Background:The prevalence of hypogonadism and associated related factors among a group of human immunodeficiency virus positive (HIV+) patients in Shiraz, Iran, were examined based on free testosterone (FT) and total testosterone (TT) levels. Objectives: In this study we planned to determine the prevalence of hypogonadism among a group of men with an HIV infection in Shiraz, Iran. Measurements of free and total testosterone levels and their association with some related factors were determined, in order to suggest new approaches in harm reduction strategies. Materials and Methods: A total of 237 males, HIV-positive patients were recruited based on convenience sampling, from May to October 2010. All patients provided their informed consent, and blood samples were collected after an overnight fast in order to measure free testosterone concentrations, HGB, luteinizing hormone (LH), follicle-stimulating hormone (FSH), and prolactine (PRL) levels. Results: A total of 180 (75%) subjects were hepatitis C virus (HCV) positive, and 23 (9.7%) subjects were HBS-positive. Based on free testosterone (FT) levels 62.8% subjects had hypogonadism, and with total testosterone (TT) levels 59.6% subjects had hypogonadism. The results showed that FT levels were associated with; age, methadone use (OR = 1.74, CI: 0.97-3.1), LH (OR = 0.91, CI: 0.87-0.95), HGB (OR = 0.788, CI: 0.69-0.89), body mass index (BMI) (OR = 0.88, CI: 0.79-0.98) and PRL (OR = 1.18(CI: 1.09-1.28), but it had no significant association with highly active antiretroviral therapy (HAART), smoking, hepatitis or reaching the AIDS stage. On the other hand, TT had a significant association with BMI, LH, PRL, and HGB. Conclusions: The prevalence of hypogonadism in the participants was high. It is recommended that a hypogonadism examination should be included in surveillance programs for HIV-positive men.