Introduction: Pilonidal sinus is a chronic recurrent disease of young adults and males are affected twice than females. Principles of surgery include complete eradication of the sinus tract; complete healing of the overlying skin, and prevention of recurrence, In this study, we used a semi-closed method, and we aimed to compare it with the open and Karydakis methods.   Patients and methods: Between January 2012 and March 2014, this prospective study included 148 patients with primary pilonidal sinus disease who were divided into three groups; group 1 (Karydakis method), group 2 (open method) and group 3 (semi-closed method). Outcome measures were operative time, length of hospital stay, rate of complications, time to return to work, time to complete wound healing, and recurrence rate.   Results: The mean operative time in group 1 was 55±5 minutes. On the other hand, it was 32±8.11 min- utes in group 2 and 36.4±3.59 minutes in group 3 (P 0.000). Healing time was significantly longer in the group treated by open method followed by semi-closed method and lastly Karydakis method with mean of 47±4.34, 22.22±7.63 days and 13±3.23 respectively (P 0.000). There were no significant differences between the three groups regarding postoperative complications except for seroma formation which was recorded lower in group two and three than in group one (P 0.002).   Conclusion: Semi-closed method is a good surgical option for the treatment of pilonidal sinus disease in terms of being simple, faster tissue healing and having better cosmetic results with low complications rate.