Background: The aim of this study was to determine the relationship between body mass index, biochemical parameters, and 5-hydroxytryptamine (5-HT) genetic polymorphisms and prostate dysfunction in an elderly general male population. Results: One hundred and seventeen elderly male subjects [60 men without symptoms of prostate hyperplasia, 42 men with untreated benign prostatic hyperplasia (BPH), and 15 men with prostate cancer (PCa)] treated with finasteride or flutamide were included. Multiple comparisons showed significant difference in age, T-score, concentration of phosphorus, calcium, C-reactive protein, and prostate-specific antigen (PSA) between the groups. T-score was the lowest and phosphorus concentration was the highest in the PCa group. Highest PSA, proteins, calcium, and Hekal's formula score were found in the BPH group. Patients with PCa were more frequent GG + GA carriers of 5-HT1B 1997A/G gene polymorphism ( p = 0.035). Univariate regression analysis showed association of PCa-treated subjects with age ( p = 0.010) and 5-HT1B genetic polymorphism ( p = 0.018). Antiandrogen therapy affects T-score ( p = 0.017), serum phosphorus ( p = 0.008), glucose ( p = 0.036), and total proteins ( p = 0.050). Multivariate-stepwise logistic regression analysis showed the significant association of treated PCa with age ( p = 0.028) and inorganic phosphorus ( p = 0.005), and a marginal association with ultrasonographic T-score ( p = 0.052). Conclusions: Antiandrogen therapy might induce bone mineral loss in elderly PCa patients. Preliminary data imply that the genetic variants of the 5-HT1B receptor might be associated with PCa.