Objective To compare endovenous laser therapy (EVLT) with endovenous microwave coagulation (EMC) in the treatment of varicose vein in the lower extremities. Methods Sixty-five (male 30, female 35) patients with 70 lower extremities (35 legs in each treatment group) were pair matched according to age, gender and CEAP classification to receive endovenous laser therapy (EVLT) or endovenous microwave coagulation (EMC). The same surgeon performed all procedures. Patients were monitored on 72 hours, 4 weeks and 6 months after the procedure (by procedural site scored for bruising, skin burn, painful induration or trabes as well as a pain score), the cured extremities were examined via Duplex uhrasonography to evaluate the effects of the procedure. Results All these 65 patients (mean age, 47.52 years) completed treatment and were followed-up. The mean operation time of EMC group was less than that of EVLT (71±25 vs. 59±15, P=0.01). At 72 hour after the procedure, bruising scores and skin buring were significantly different (P<0.05): patients in the EMC group showed less bruising (17.14% vs. 54.29%) but more burn (48.57% vs. 20%) on the procedure site than the patients in the EVLT group. At 4 weeks and 6 months after the procedure, no significant differences were found between patient outcomes, physical conditions, and symptoms and or possible adverse events. In 20/28 patients the pigmentation faded away, Edema were relieved in all the 25 extremities. 4 patients with ankle ulcer were healed. No major complications were found. Conclusions Both EMC and EVLT were effective in treating lower extremities varicose veins, with no major complications.