Introduction & Objective: The aim of this study was to compare the results of pilonidal sinus surgery with primary closure versus open method.Materials & Methods: In a randomized clinical trial, all the patients with the diagnosis of chronic natal cleft pilonidal sinus, referring to the surgical clinic of Shariati Hospital during 2007 - 2008 were included.They underwent either excision with midline closure (primary closure, n=40), or excision without closure (open wound management, n=40). Patients who came with an acute pilonidal abscess were excluded from the study. The recorded outcomes were hospital stay, healing time, off work period, postoperative pain, patient’s satisfaction and the recurrence rate.Results: The majority of patients were male in both groups (87.50%). There was no significant difference in the hospital stay. Off work period (8.65±1.73 vs.11.53±2.33 days, P=0.001) and healing time (3.43±0.92 vs.5.3±0.79 days, P=0.001) were shorter in the primary closure group; but, there were no significant differences in their hospital stay and number of visits. The intensity of postoperative pain in the 1st (37.75±6.5 vs.43.63±5.06, P=0.001), 2nd (26.75±6.66 vs.34.63±5.48, P=0.001), 3rd (18.25±6.05 vs.27.88±6.88, P=0.001), and 7th (8.45±3.85 vs.17.88±6.19, P=0.001) days were lower in the primary closure group.Statistically there was no significant difference in the complication and recurrence rate between the two groups. Patients’ satisfaction was higher in the primary closure group (4.15±0.53 vs.3.6±0.5, P=0.001).Conclusions: According to the results of this study, excision and primary closure is the preferred procedure in the management of patients with pilonidal sinus. It has the advantages of shorter time off work, earlier wound healing, lesser postoperative pain, higher patients’ satisfaction, while complication and recurrence rates are comparable with open method.