Two methods for treatment of chronic pilonidal disease were compared in a randomised trial of 100 patients with a mean follow-up of 29 months. Four patients were excluded from the excision and closure group, leaving 96 patients for analysis. Initial primary healing was significantly more frequent after excision and primary closure (45/46; 98%) compared with excision and healing by secondary granulation (36/50; 72%). The mean healing time was significantly shorter in the excision and closure group (10.3 days) compared to the excision and granulation group (13 weeks). There was, however, no significant difference between the two groups in cure rate after the first operation. The recurrence rate in the excision and granulation group was 12% and after primary closure 20%. The presence of stiff hair and anaerobic bacteria were related to the failure of primary healing, but not associated with recurrence. Although the cure rate was the same regardless which operation was done, the primary healing was quicker and the healing time and duration of sick-leave were shorter after primary closure. Excision with primary closure therefore seems to be the preferable method.