Two prospective studies were undertaken to examine the role of bacteria in the outcome after excision and primary suture for chronic pilonidal sinus disease. In the first study 52 consecutive patients were given cloxacillin as prophylaxis. In a second randomised study 51 patients were given 2 g cefoxitin intravenously (n = 25) or no prophylaxis (n = 26). From 49 out of 98 patients (50%) no microorganisms were isolated from sinuses preoperatively. Wound complications were observed postoperatively in 61% of the patients (63/103). A postoperative bacteriology sample was positive in 47 of 49 samples (96%). Preoperative presence of bacteria was not significantly associated with wound complications. Anaerobe isolates were present in 40% of patients preoperatively whereas aerobes were cultured in 43% postoperatively. After an observation period of 30-42 months, recurrences were 13% among the patients (7/52) who had been given cloxacillin. No recurrences were seen in the last study after an observation period of 18-30 months, for an overall 7% in both studies. We conclude that preoperative bacterial isolates, usually anaerobes, in chronic pilonidal sinuses do not influence the complication rate since bacterial isolates from infected wounds are mostly aerobes.