Objective: To prospectively evaluate the intraoperative and post-operative utility of the Cook–Swartz Doppler flow monitoring system for free flap monitoring of arterial and venous anastomosis in head and neck reconstruction of oral cavity defects. Study design and setting: A cohort of consecutive patients with oral cavity defects requiring free-tissue transfer flap reconstruction by the Division of Otolaryngology-Head and Neck surgery at the University of Alberta Hospital were followed prospectively. The intervention in all patients was the use of implantable Cook–Swartz Doppler probe systems for monitoring both the arterial and venous microvascular anastomoses while concurrently collecting a battery of traditional clinical markers for free flap viability. These patients were group matched by flap type, age and gender to a cohort of patients who underwent free-tissue transfer flap reconstruction with single vessel implantable Doppler monitors. Data were collected at the time of surgery and for the ten post-operative days while the Doppler system was in situ regarding flap compromise, salvage, impaired flow as determined by the Doppler monitoring system and any intervention or re-operative findings. Results: When compared with the matched single Doppler cohort, the double Doppler group had an increased rate of intraoperative modifications but a significantly lower rate of surgical re-explorations, a lower need for revising the anastomosis and a lower rate of flap failure. Conclusions: This study supports the utility of a two-vessel monitoring system for intraoperative detecting in adequacy of vascular anastomosis. In the post-operative period, while the Doppler system was associated with false positives, reassuring Doppler signals were often used to prevent unnecessary surgical re-exploration in addition to earlier detection of compromise leading to improved rates of salvage.