The prevalence of hypogonadism in HIV patients is still a matter of debate. Today, serum free testosterone (fTST) is thought to be more important than serum testosterone in the diagnosis of hypogonadism in patients with HIV. This study aimed to determine the prevalence of low fTST levels and the effects of anti-retroviral therapy (ART) on fTST levels in treatment-naïve male Japanese patients with HIV. Patients who visited Teikyo University Hospital, Japan between 2010 and 2016 were enrolled. Patients' fTST levels were evaluated twice with a radioimmunoassay in the morning, at the onset of ART and one year later. Clinical factors were also reviewed. The patients were divided into two groups ('hypogonadism' and 'normal') based on Japanese criteria. To determine factors related to low fTST in treatment-naïve patients, the Mann-Whitney U test and a multiple-regression analysis were used. Changes in fTST levels after ART initiation were evaluated with a paired t-test. Data from 25 patients were collected. Their median age was 36.0 years, and the median fTST level was 8.00pg/ml in the treatment-naïve state. Thirteen patients (52%) were in the hypogonadism group. Low levels of fibroblast growth factor 23 were significantly related to low fTST levels. After the start of ART, fTST levels increased significantly (median 8.00 interquartile range [6.40-9.70] to 9.60 [7.60-13.10] pg/ml, p=0.0081). Subnormal fTST levels occurred frequently among the present study patients in treatment-naïve settings. Free testosterone levels in patients with HIV were significantly increased one year after the start of ART.