Composite free tissue transfer has an established role in head and neck oncology for the reconstruction of the bony defect following tumor ablation, and while donor-site morbidity is variably reported, there is little consensus on the most favorable donor site. The fibula and deep circumflex iliac artery have distinct advantages in terms of the volume and length of bone in mandibular reconstruction. Few studies have compared their donor-site morbidity. The aim of this study was to compare the fibula and deep circumflex iliac artery flaps using a review of the case notes and cross-sectional review of patients attending a research clinic for validated orthopedic examination and completion of health-related quality-of-life questionnaires. Between February of 1993 and May of 2001, 44 fibula free flaps and 73 deep circumflex iliac artery free flaps were performed. Ninety-nine case notes and 36 patients were available for review of donor-site morbidity. Sixteen patients with fibula flaps and 20 patients with deep circumflex iliac artery flaps took part in the clinical examination component of the study, which was composed of a clinical examination by an orthopedic surgeon using the American Orthopedic Foot and Ankle Society ankle scoring system and the Harris hip scoring system, and two patient-completed questionnaires, the University of Washington Questionnaire and the Hospital Anxiety and Depression Scale. Subjective and objective markers of morbidity related to both flaps were similar in most parameters. However, fibula flaps were associated with more problems with donor-site healing, reduced power, and sensation. Poor orthopedic scores for both flaps were associated with notably poor scores on the University of Washington Questionnaire and the Hospital Anxiety and Depression Scale. The study would suggest that both deep circumflex iliac artery and fibula donor sites result in an acceptable and comparable morbidity for most patients, but in cases in which significant donor-site morbidity is encountered, health-related quality of life is significantly compromised.