Objective To compare transurethral microwave thermotherapy (TUMT) with urethral cooling in a high-energy protocol (Prostatron(TM) version 2.5), with transurethral resection of the prostate (TURF) for the treatment of symptomatic, uncomplicated, urodynamically obstructive beni,an prostatic hyperplasia (BPH). Patients and methods Patients with moderate to severe symptomatic, uncomplicated BPH, unequivocally obstructed as assessed from the Abrams-Griffith nomogram, who were technically suitable for either form of treatment, were randomized into two groups of 30 patients each to undergo either TUMT or TURF. Five efficacy variables, i.e. the American Urological Association (AUA) symptom score, maximum flow rate (Qmax), post-void residual urine volume (PVR), voiding pressure at maximal now (Pdet max) and prostatic volume determined by ultrasonography (PV) were measured initially and 6 months after treatment using a defined protocol. Complications were recorded during and up to 6 months after the treatment. As the variables were independent, the data were analysed using a paired t-test for each to assess the treatment effect for each group. Results After TURF, all the variables improved significantly; after TUMT, the symptoms improved both clinically and statistically (P<0,001), with the mean AUA symptom score decreasing from 18.4 to 5.2. However, none of the objective variables improved after TUMT, The energy delivered under software control correlated poorly with prostatic volume (r= 0.322). TUMT had considerably lower morbidity than TURF, but failure of ejaculation occurred in four of 18 sexually active men after TUMT. Conclusions Despite considerable improvement in their symptoms, TUMT using the Prostatron and Prostasoft v2.5 did not alleviate obstruction in patients with BPH. Patients treated using TUMT controlled by this software should be informed of the possibility of ejaculatory dysfunction.