Objective: To establish the bacterial flora of the perineum before and after antiseptic preparation in male urology patients. Patients/Methods: Adult male patients undergoing cystoscopic procedures were studied. Three sets of swab specimens, labelled A, B and C, were taken from the perineum in the theatre. Specimen A was taken before cleaning and disinfection of the skin with Savlon® (Chlorhexidine- cetrimide mixture), specimen B after disinfection and draping, and C after completion of the operative procedure. Specimens were processed on standard laboratory media for aerobic and anaerobic bacteria and yeasts. Results: Of the 114 patients studied, 43 (37.7%) had a positive culture for significant microorganisms in specimen A, 7 (6.1%) in specimen B and 13 (11.4%) in specimen C (A vs. B p < 0.001, A vs. C p < 0.001, B vs. C p < 0.01). The commonest isolates in specimen A wereGram-positive organisms (84.1%). The positive-culture rate for patients with end-stage renal failure was 71.4%, for those with a urethral catheter it was 53.8%, for those without systemic diseases it was 36.6% and for patients with diabetic mellitus it was 28.1%. Conclusion: About 38% of patients undergoing cystoscopic procedures had a significant positive perineal culture, with Staphylococcus species being the predominant skin flora. The bacteria culture rate was affected by the presence of systemic diseases. The use of Savlon to disinfect the perineum resulted in a significant reduction in the bacterial count of the perineum.