Abstract : To determine the advantages and disadvantages of flap reconstruction surgery and open excision with direct closure method for treatment of pilonidal sinus. The article presents materials on prospective observational study of 50 patients of pilonidal sinus of which 25 patients underwent flap reconstruction and the other 25 underwent open excision and primary closure. Time taken for complete healing and return to work were recorded. Post operative complications such as (wound infection, collection, dehiscence) were more common in open excision group than in the flap reconstruction group. Mean follow-up was 6 months. A significant difference was observed between the two groups in terms of length of hospital stay, time taken for complete healing, wound infection(P<0.001), recurrence rates. In flap group the infection, wound dehiscence and recurrence are lower than the open group. Flap reconstructions were superior to primary closure after excision of pilonidal sinus and that Limberg flap was superior with regard to wound infection and recurrence.