A study is planned to compare the superiorities of each other, V-Y and Limberg flap methods which are two popular methods in surgical treatment of pilonidal sinus with wide excision is required, considering the current literature. Method: The study included 100 patients which are diagnosed with pilonidal sinus disease and flap planned due to the width of defect. Patients were divided into two groups randomly. 50 patients were treated with the V-Y flap procedure in group A and 50 patients were treated with Limberg in group B. Both groups were prospectively followed in terms of complications, recovery times, loss of work power, patient satisfaction and 2 year recurrence rates, and the findings were compared statistically. Results: Demographic characteristics, complaints and clinical findings were similar in both groups. Postoperative wound infection rates were close (26%, 28%; p>0,005) but wound separation was seen more in Limberg group (26%, 36%; p<0,005). Wound healing process, loss of work power were longer in Limberg flap group, but the results were not statistically significant. There was no difference between groups about patients' satisfaction and 2-year recurrence. Conclusion: The long-term recurrence rates of V-Y flap and Limberg flap technique are similar. Wound separation is significantly less in V-Y flap technique. According to the results of this study, V-Y flap method can be accepted as a better alternative after excision which causes wide tissue loss.