Background & aim: Many operative methods have been described for treatment of pilonidal sinus, however, no one is completely satisfactory. The Aim of this study was to compare modified Limberg flap transposition versus Karydakis flap reconstruction in patients with sacrococcygeal pilonidal disease. Methods: A prospective randomized study was conducted on 40 patients with denovo sacrococcygeal pilonidal diseases at General Surgery Department in Tanta University Hospitals throughout the period from June 2013 to June 2014. The patients were randomly divided into two groups: Group “A" (The patients subjected to modified Limberg flap transposition) and Group “B" (The patients subjected to Karydakis flap reconstruction). This study Compares results of wound infection, wound disruption, wound haematoma, duration of surgery, time of hospital stay and recurrence rate. Results: The majority of our patients were males(85%), drivers(48%),with no significant difference between the two groups regarding duration of surgery or hospital stay. 5% of the patients in group “A" developed wound infection versus 25% in group “B" while no patient in group “A" developed wound disruption versus 20% in group “B". No patient in group “A" had recurrent disease versus 15% in group “B" and this difference was statistically significant. Conclusion: Modified Limberg flap had a superiority over Karydakis flap in the ability to excise all tracts if extensive pilonidal sinus, low incidence of wound infection, and wound disruption, shorter hospital stay with no recurrence. We recommend the use of modified Limberg flap in the treatment of pilonidal sinus disease.