Controversy still exists regarding the best surgical technique for the treatment of pilonidal disease in terms of minimizing disease recurrence and patient discomfort. The present study analyzes the results of excision with primary closure and excision with flap reconstruction in the surgical treatment of sacrococcygeal pilonidal disease. From January 2003 to January 2006, 60 consecutive patients with primary pilonidal sinus disease received surgical treatment in the form of either excision and primary closure (group I, n = 20 patients) or excision and flap reconstruction (group II, n = 40 patients; modified Limberg flap n = 20, classic Limberg flap n = 10 and adipo-fasciocutaneous flap n = 10). Times for complete healing and return to work were recorded. To evaluate patient comfort, all patients were asked to complete a questionnaire including visual analog scale, time to sitting on toilet without pain, and time to walking without pain 3 months after surgery. Mean follow-up was 21 months. A significant difference was observed between the two groups in terms of length of hospital stay (P < 0.003), time to complete healing (P < 0.001), time off work (P < 0.001), wound infection (P < 0.01), recurrence rates (P < 0.01), times to sitting on toilet without pain (P < 0.002), and walking without pain (P < 0.001). The mean (standard deviation) postoperative visual analog scale scores were 6.1 (1.2) in the primary closure group vs. 7.4 (1.3) in the flaps groups (P < 0.001). In the modified Limberg flap, no wound infection, wound breakdown, or recurrence of the disease occurred. Flap reconstructions were superior to primary closure after excision of pilonidal sinus and that modified Limberg flap was superior with regard to wound infection and recurrence.