PURPOSE: In this study, we investigated whether there is a factor that can aid determi nation of the preferred technique by comparing the early and late results of two different surgical techniques for the treatment of pilonidal sinus. METHODS: The medical records of 176 patients in whom the Limberg flap (LF) or V-Y flap techniques were applied for reconstruction after the excision were evaluated retrospectively. RESULTS: The development rates of postoperative hematoma, wound separation, wound infection, and seroma were 2.8%, 5.1%, 5.6%, and 6.3%, respectively, while total flap necrosis was not observed in any patient. Return to daily activities was achieved after a mean of 17.1 days (13 to 21 days) days in the LF group and 32.7 days (18 to 47 days) in the V-Y flap group. During the average follow-up of 65 months (36 to 110 months), nine patients (5.1%) developed recurrent disease. There was no difference between the two groups with respect to early surgical complications (P = 0.286) or disease recurrence (P = 0.094), whereas the resumption of daily activities was longer in patients with a V-Y flap (P < 0.001). CONCLUSION: The early postoperative and long-term results of the LF and V-Y flap techniques for the treatment of pilonidal sinus were similar. Because the resumption of daily activities at work is achieved later in patients undergoing the V-Y flap compared with the LF technique, patients' employment (or position in working life) must be considered when determining the most appropriate surgical technique.