Sex steroids are known to modulate serum lipoproteins. Studies have suggested that serum testosterone levels are associated with a beneficial lipid profile. Androgen deprivation therapy (ADT) is employed in the treatment of recurrent and metastatic prostate cancer (PCa), resulting in profound hypogonadism. As male hypogonadism unfavorably influences lipid profile and men with PCa have high cardiovascular mortality, we evaluated the effects of long-term ADT on fasting lipids. This Cross-sectional study was conducted in a university-based research institution. We evaluated 44 men, 16 undergoing ADT for at least 12 months before the study (ADT group), 14 age-matched eugonadal men with non-metastatic PCa who were status post prostatectomy and/or radiotherapy and not on ADT (non-ADT group) and 14 age-matched eugonadal controls (Control group). None of the men had known history of diabetes or dyslipidemia. Mean age was similar in the three groups (P ¼ 0.37). Serum total (Po0.01) and free (Po0.01) testosterone levels were lower in the ADT group compared to the other groups. Men on ADT had higher body mass index (BMI) compared to the other groups (Po0.01). Men in the ADT group had significantly higher levels of total cholesterol compared to the other two groups (P ¼ 0.03). After adjustment for BMI, men on ADT continued to have significantly higher fasting levels of total cholesterol (P ¼ 0.02), LDL cholesterol (P ¼ 0.04) and non-HDL cholesterol (P ¼ 0.03) compared to the control group. No significant differences were seen in the levels of other lipoproteins between the three groups. These data show that men undergoing long-term ADT have higher total and LDL cholesterol than age-matched controls. Long-term prospective studies are needed to determine the time of onset of changes in these lipoproteins while on ADT and the influence of these changes on cardiovascular mortality.