Both of latissimus dorsi and rectus abdominis muscles are workhorse for various reconstructive surgeries. These muscle flaps have been used widely for soft tissue coverage, tissue augmentation, and functional muscle transfer. However, the traditional method for muscle harvest requires a long incision that often results in an unsightly scar and becomes the main concern of the patient. The purpose of this study is to introduce our clinical experience of endoscopic harvest of latissimus dorsi muscle and rectus abdominis muscle, and to make comparison with traditional harvest of these two muscle flaps. Of the 13 rectus abdominis muscles free flaps, 6 muscles were harvested traditionally and 7 muscles were harvested with endoscopic assistance. Of the 21 latissimus dorsi muscle free flaps, 12 muscles were harvested traditionally and 9 muscles were harvested with endoscopic assistence. Follow up period was between 6 months and 24 months. The patients age ranged from 7 to 70 years old. The result revealed no statistically significant differences in the amount of intraoperative bleeding, incidence of postoperative hematoma and seroma, and the incidence of donor-site wound infection. However, patients feel less pain and start earlier and better movement after the operation with endoscopically assisted harvest. This technique is easy to learn, is safe, and can reduce substantially the donor site morbidity comparing traditional harvesting technique.