Background: Open window thoracotomy (OWT) as well as its closure are challenging. Transposition of omental pedicle and muscle flaps is often performed for OWT closure; however, the better technique among the two is unknown. The purpose of this series was to evaluate the outcomes of using both omental pedicle and muscle flaps for the aforementioned closure. Results: There were 9 (33.3%) omental pedicle flap procedures and 18 (66.7%) muscle flap procedures.The rate of local recurrence after closure of OWT was significantly higher with muscle flap than with omental pedicle flap (0% vs. 50.0%, P=0.012). The median duration of postoperative hospital stay was significantly shorter with omental pedicle flap than that with muscle flap (16.0 vs. 41.5 days, P=0.037).Mortality was observed in 2 patients (11.2%) in the muscle flap group and no patient in the omental pedicle flap group. Success rate was similar between the two groups (100% for omental pedicle flap vs. 83.3% for muscle flap).Conclusions: Omental pedicle flap was superior to muscle flap in terms of reducing local recurrence and shortening postoperative hospital stay. However, mortality, morbidity and success rates were not affected by the choice of flap.