Background: The ideal operation for pilonidal sinus disesase should be a simple one with low complication and recurrence rates. The aim of this study was to compare the efficiency and the results of the karydakis flap with that of the limberg flap for treating pilonidal sinus disease in zagazig university hospitals. Objectives: To study the post-operative results and the effectiveness of Karydakis and Limberg flaps in the treatment of pilonidal sinus disease.Methods:20 patients were enrolled in this interventional comparative clinical study and were divided into two equal groups.Group (1) were operated on via the the karydakis flap and group (2) via the limberg flap.Results: The mean operative time was shorter with the Karydakis group (41.7 ± 4.22minutes) than with the Limberg group (51.5 ± 4.17minutes). There was no significant difference between both groups regarding overall complication rate .The mean time off work was shorter with the Karydakis procedure(14.6 ± 2.46 days).The healing time was significantly shorter with the Karydakis group than with the Limberg group(18 ± 3.05 vs 21.6 ± 3.41 days, P= 0.023). The visual analogue score for the cosmetic satisfaction of patients in the Karydakis group was 7.8 ± 1.03, whereas it was 4.2 ± 0.92 in the Limberg group with a p value( < 0.001).Only one patient(10%) from each group developed recurrence.Conclusion: Karydakis flap procedure should be chosen instead of Limberg flap because of its shorter operative time, earlier return to work, faster healing time with lesser incidence of wound disruption and significantly higher patient satisfaction.