Pilonidal sinus disease (PSD) is a common infection of the skin in the natal cleft, with a prevalence of 0.7% in the general population. Pilonidal sinus can occur in many different areas of the body but most are found in the sacrococcygeal area, in the natal cleft, approximately 5 cm from the anus. Pre-study power analysis revealed that a sample size of total 60 patients; 30 in each arm. The perfect approach for the management of PNS should be simple, cause minimal pain, have best chance for success and least recurrence rate with low risk for complications, require minimal wound care, and ensure minimal inconvenience for the patient with rapid return to normal activity. This is a prospective randomized study conducted at Department of General Surgery, Ain shams university and Imbaba General hospital to compare the modified sinotomy with marsupialization versus excision with lay open in treatment of pilonidal sinus disease. 77% of the participants were males aged from 17-52. Operative time in modified sinotomy group ranged from 20-40 minutes and in lay open group ranged from 20-35 min with no significant difference was found between the two groups in terms of operative time (P-value: 0.07). There was significant difference between the 2 groups in time to return to work in favour of ms group (a mean of 3.6 weeks compared with a mean of 6.7 weeks for the lay open group with a P value <0.0003. In conclusion, we believe that execution of a minimal surgical technique for PSD can be among the most important methods for treating not only primary PSD but also complicated cases and modified sinotomy is a very simple surgical procedure for treatment of psd in terms of early return to work.