Several microvascular free flaps are available for reconstruction of the osseous components after resections for head and neck cancer. We have prospectively evaluated patients treated by bony microsurgical reconstruction to identify predictors of adverse outcomes for delayed wound healing and failure of free flaps. All patients from July 2007 to June 2011 who had reconstructions with microvascular fibular or iliac crest flaps immediately after resection of the tumour were evaluated. There were a total of 156 bony free flaps: 120 (77%) fibular and 36 (23%) iliac crest flaps. A total of 133 (85%) were successful. Delayed wound healing was more common with the iliac crest flap (p=0.01) at the intraoral site (p=0.04). Significantly more iliac crest free flaps failed (p=0.02). Anastomosis to the facial artery (p=0.05) and facial vein (p=0.04), and duration of overall operating time were associated with a significantly higher risk of failure of the flap. Patients with cancer of the head and neck who require microsurgical bony reconstruction are at increased risk of postoperative complications. Significantly more complications were found with the iliac crest flap, whereas the fibular flap was associated with a significantly longer operating time.