Purpose: Pilonidal sinus is a frequent disease that occurs mostly in hairy young men, defined as chronic inflammation and infection of the postsacral sinuses. Wide excision of the affected area is the treatment of choice. Many techniques have been described to cover the defect. However none appears to be the ideal procedure to prevent infection, recurrence, and delayed wound healing. We present the results of an alternative technique that we performed by using partial deepithelized gluteal transposition flap for reconstruction of the defect following wide excision. Methods: From October 2004 to September 2007, we performed the partial deepithelized gluteal transposition flap method on 6 patients. We modified the transposition flap techniques by deepithelialising the medial parts of the flap and burying them under the opposing edge of the flap. The results were compared with previous studies and evaluated regarding duration of surgery, size of defect, hospitalization periods, and complications. Results: All the flaps were healed well with no partial or complete loss of the flap. Hospitalization and immobilization periods were acceptably shortened. Recurrence was not seen. The aesthetic outcome was also satisfactory and all patients were satisfied with the results. Conclusion: The main advantage of our techniques is using healthy tissues to obliterate the dead space, to provide an extra-cushion, and to prevent deep dehiscence. We believe that the partial deepithelized gluteal transposition flap is a good alternative method for treatment of pilonidal sinus.