Waist circumference is considered a useful predictor of obesity-associated cardiovascular risk, but its use as an indicator of sexual health status and quality of life (QoL) in hypogonadal men is unknown. We investigated whether three measurements of obesity, weight, body mass index and waist circumference, correlate with the International Index of Erectile Function-5 (IIEF-5), the Aging Males' Symptoms (AMS) and the International Prostate Symptom Score (IPSS) questionnaires. A total of 261 patients were enrolled in a prospective study on hypogonadism treatment with intramuscular long-acting testosterone undecanoate. Patients with total testosterone ≤3.5 ng ml(-1) were enrolled, and baseline demographic data were recorded. Patient's response to IIEF, IPSS and AMS standardised questionnaires was recorded to evaluate health-related QoL. The mean length of treatment and follow-up was 4.7 years (max 6 years). ANOVA regression analysis showed that waist circumference was significantly inversely proportional to IIEF-5 and directly proportional to AMS and IPSS. Weight was inversely proportional to IIEF and directly proportional to IPSS but not associated with AMS. BMI had no proportionality to measurements of sexual function and quality of life. These results suggest that among weight, BMI and waist circumference, the latter is the best predictor of health-related QoL in men with hypogonadism.