Objectives: To determine the incidence of hypogonadism in men with human immunodeficiency virus (HIV)/acquired immunodeficiency virus (AIDS), the most useful serum testosterone measurement and threshold for diagnosing hypogonadism, and the comparative efficacy of 2 testosterone replacement therapy (TRT) 1% gels (AndroGel (R) [Abbott Laboratories] and Testim (R) [Auxilium Pharmaceuticals, Inc.]). Design and Subjects: This was a 2-stage observational study. In stage 1, patient records from 2 medical practices specializing in HIV/AIDS were reviewed. Eligible patients were aged >= 18 years; had HIV-seropositive status confirmed by enzyme-linked immunosorbent assay and western blot test or HIV-1 viremia confirmed by HIV-1 RNA polymerase chain reaction; and had prior baseline testosterone assessments for hypogonadism (ie, presence of signs/symptoms of hypogonadism as well as total testosterone [TT] and free testosterone [FT] level measurements). Stage 2 included the evaluation of patients from stage 1 who were treated with 5 to 10 g/day of TRT. The stage 2 inclusion criteria were a diagnosis of low testosterone (defined as TT level, 300 ng/dL and/or FT level, 50 pg/mL, as per The Endocrine Society guidelines and presence/absence of hypogonadal signs and symptoms); >= 12 months of evaluable sign and symptom assessments and TT/FT level measurements while on TRT with either Testim (R) or AndroGel (R); and >= 4 weeks on initial TRT if the initial TRT was switched or discontinued. Results: Four hundred one of 422 patients met the stage 1 inclusion criteria and 167 of 401 patients (AndroGel (R), n = 92; Testim (R), n = 75) met the stage 2 inclusion criteria. Total testosterone level < 300 ng/dL alone identified 24% (94 of 390) of patients as hypogonadal, but failed to diagnose an additional 111 patients (67.7%) with FT levels < 100 pg/mL and hypogonadal symptoms. Through month 12, AndroGel (R) increased mean TT levels by +42.8% and FT levels by +66.9%, compared with +178.7% (P = 0.017) and +191% (P = 0.039), respectively, for Testim (R). Patients treated with Testim (R) showed significantly greater improvements in libido, sexual performance, nighttime energy, focus/concentration, and abdominal girth, and trends for greater improvement in fatigue and erectile dysfunction than patients treated with AndroGel (R). No patients discontinued therapy due to adverse events. Conclusion: The most useful serum testosterone measurement and threshold for diagnosing hypogonadism in men with HIV/AIDS was FT level= 1 hypogonadal symptom. This is above currently accepted thresholds. Criteria using TT level < 300 ng/dL and FT level < 50 pg/mL only diagnosed 24% and 19% of patients, respectively, as having hypogonadism. Testim (R) was more effective than AndroGel (R) in increasing TT and FT levels and improving hypogonadal symptoms.