Background: Controversy exists regarding the optimum treatment for pediatric pilonidal disease. It is a complex disease process with a high rate of recurrence. A spectrum of surgical strategies exists, including drainage, cyst marsupialization, complete cyst and sinus tract excision with primary versus secondary closure, and excision utilizing flap closure. There is little published in the pediatric literature; therefore, we reviewed our experience in an attempt to document how various interventions affect the natural history. Methods: A retrospective review was conducted in which all patients who underwent surgical intervention for pilonidal disease at our institution from January 2000 to June 2010 were identified. Data collection included demographics, surgical procedure performed, presence of wound breakdown, presence of infection, recurrence, total procedures performed, number of follow-up visits, and total hospital days. Results: In the study period, 120 patients were identified, and 58% were female. Mean age was 14.9 y old (1-19 y). These patients were then subdivided into closed versus open groups based on the status of their operative wound. In the closed group, 74 patients underwent excision with midline closure and 18 underwent excision with flap closure. There were 28 patients left open after excision. In the closed group, wound breakdown occurred in a total of 41 patients (45%). There was no difference in breakdown between midline and flap closure. Postoperative wound infection occurred in 15% of all patients. The midline closure group had a higher infection rate (20%) compared with those with flap closures (11%), which was not significant (P = 0.30). There was no difference in recurrence rate between patients who were primarily closed and patients who were left open (20.6% versus 25%, P = 0.51). There was also no difference in their hospital length of stay (0.44 ± 2.53 d versus 1.18 ± 2.9 d, P = 0.18). Conversely, the patients who were left open had more follow-up visits (6.48 ± 7.6 versus 4.18 ± 3.3, P = 0.02) and subsequently required more operative procedures (1.71 ± 1.12 versus 1.25 ± 0.49, P = 0.002). Conclusion: Management of pilonidal disease remains a complex problem, and operative intervention is fraught with complications, including wound breakdown, infection, and cyst recurrence. Primary closure appears to have better outcomes compared with healing by secondary intention. There does not appear to be a clear advantage of primary closure utilizing flaps over primary closure based on our early experience with flap closures. © 2011 Elsevier Inc. All rights reserved.