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The study was carried out to compare the efficacy of subfascial endoscopic perforator surgery (SEPS) and open subfascial ligation of perforators in varicose veins. This study was conducted on 100 patients of varicose veins from January 2006 to December 2010. Clinical scoring and color Doppler were performed in all the patients before surgery. Patients were divided into two groups: Group A and Group B alternately. Management of the perforators was done by subfascial endoscopic perforator surgery (SEPS) in Group A and by open subfascial ligation of perforators in Group B. Fifty patients were treated in each group. All the patients underwent ligation of incompetent saphenofemoral junction with stripping of long saphenous veins wherever the junction was incompetent with multiple ligation of superficial prominent veins. SEPS was done by two-port method without any tourniquet or balloon dissector. Total numbers of perforators ligated were 178 in Group A and 136 in Group B. Patients in both the groups got symptomatic relief of symptoms, but ulcer healing in 33 % patients in Group A was faster as compared to Group B. However, at 3 months of follow-up the ulcers healed in all the patients in both groups. Incidence of wound infection was higher in group B (16 %) as compared to group A (0 %). There were residual perforators in 8 % of patients on color Doppler at 3 months of follow-up in Group B while there was no residual incompetent perforator in Group A. Subfascial endoscopic perforator vein surgery is a safe and effective method for treating incompetent perforating veins. The number of perforators ligated in SEPS was more as compared to the open subfascial ligation group. Possibly some perforators may be missed on Doppler localization and missed ligation, which may be a cause of future recurrence in varicose veins. Early relief of symptoms in terms of ulcer healing was better in the SEPS group with less wound complication rate; however, all the ulcers healed in both the groups at 3 months of follow-up. Cosmetic results were equal in both the groups. Major advantage of SEPS was less incidence of wound complications and less incidence of residual incompetent perforators. Hence, SEPS should be added for the management of perforators along with conventional surgery in varicose veins.