PURPOSE: We compare directly the efficacy and safety of targeted high energy transurethral microwave thermotherapy with alpha-blocker treatment for benign prostatic hyperplasia (BPH). MATERIALS AND METHODS: In this randomized prospective study 52 patients with symptomatic BPH received terazosin and 51 underwent high energy transurethral microwave therapy with topical anesthesia. Patient evaluation included determination of International Prostate Symptom Score (I-PSS), peak flow rate and quality of life score before transurethral microwave therapy or terazosin and periodically up to 6 months thereafter. RESULTS: At 2-week followup the terazosin group transiently exhibited significantly greater improvement than the transurethral microwave therapy group in mean values of all 3 primary efficacy parameters of I-PSS, peak flow rate and quality of life score. At 12 weeks and 6 months this pattern was reversed, and the transurethral microwave therapy group achieved significantly greater improvement than the terazosin group in mean I-PSS, peak flow rate and quality of life score. By 6 months 78.4, 64.7 and 84.3% of the transurethral microwave therapy group demonstrated a 50% or greater improvement in I-PSS, peak flow rate and quality of life score, respectively, compared with 32.7, 9.6 and 40.4% of the terazosin group, respectively. Nine patients in the terazosin group and 1 in the transurethral microwave therapy group withdrew from study because of side effects or lack of treatment efficacy. CONCLUSIONS: Terazosin afforded more rapid improvement in symptoms, voiding function and quality of life in BPH patients. High energy transurethral microwave therapy offered markedly superior clinical outcomes at 12 weeks to 6 months.