Surgeons conventionally use electrocautery dissection and surgical clip appliers to harvest free flaps. The ultrasonic Harmonic Scalpel is a new surgical instrument that provides high-quality dissection and hemostasis and minimizes tissue injury. The aim of this study was to evaluate the effectiveness and advantages of the ultrasonic Harmonic Scalpel compared to conventional surgical instruments in free flap surgery. This prospective study included 20 patients who underwent head and neck reconstructive surgery between March 2009 and May 2010. A forearm free flap was used for reconstruction in 12 patients, and a fibular flap was used in 8 patients. In half of the patients, electrocautery and surgical clips were used for free flap harvesting (the EC group), and in the other half of the patients, ultrasonic dissection was performed using the Harmonic Scalpel (the HS group). The following parameters were significantly lower in the HS group compared to the EC group: the operative time of flap dissection (35% lower in the HS group), blood loss, number of surgical clips and cost of surgical materials. This study demonstrated the effectiveness of the Harmonic Scalpel in forearm and fibular free flap dissections that may be extended to other free flaps.