We studied 85 men with moderate to severe symptoms of benign prostatic hyperplasia (BPH) who completed two placebo-controlled studies of drug therapy. During the 48 week period of treatment and follow-up the patients underwent 164 procedures which included urethral instrumentation, predominantly without antibiotic prophylaxis, and 187 procedures of urethral instrumentation in combination with transperineal prostate biopsy with antibiotic prophylaxis. The risk for a patient to acquire clinically significant urinary tract infection was 2.4% after urethral instrumentation alone and 7.5% when urethral instrumentation was combined with prostate biopsy. Invasive urodynamic examinations of prostate biopsies in studies of new treatment modalities for BPH should only be performed when necessary to obtain important information, and after full informed patient consent. The combination of prostate biopsy and urethral instrumentation increases the infection rate considerably and should be avoided.