The role of natal cleft depth in postoperative morbidities after pilonidal sinus disease (PSD) surgery is still uncertain. To examine the correlation between natal cleft depth and postoperative morbidities after different methods of excision of PSD. We prospectively examined data of 66 operated patients with PSD at Prince Fahd Ben Sultan hospital, Tabouk, KSA. Of the studied patients, 18 were treated by simple closure (27.3 %), 13 patients by Bascom closure (19.7 %), 21 patients by the open method (31.8 %) and 14 patients by the semiopen method (21.2 %). Postoperative morbidities were recorded. The data were analyzed using appropriate statistical tests. Sixty six patients (62 males, 4 females) underwent surgery for PSD. The mean age of the studied patients was 26.7±6.9 (range 15-51). Nine patients (13.7 %) showed delayed healing with the highest incidence was among patients treated by the open method (6/21 (28.5 %)), and 5 patients (7.5 %) showed recurrence. There have been significant positive correlations between natal cleft depth and delayed healing, which was evident among patients treated by the open method (r0+0.78; p<.0001). The findings suggest that natal cleft depth is a significant factor correlated with postoperative morbidities of PSD after surgical treatment.