Background: Congenital anomalies are defined as structural or functional anomalies that occur during intrauterine life. Awareness of such variations will decrease intraoperative dilemma and complications. In this article, we have presented our experience in congenital anomalies and anatomical aberrations in head and neck malignancies. We have reviewed the literature and discussed relevant embryology and their clinical significance. Methods: All patients with head and neck malignancies operated at our institution in the past three years, who had congenital anomalies and anatomical aberrations detected during preoperative evaluation or intraoperatively were included in this study. Results: Seven types of congenital anomalies were encountered, with most common anomaly being the aberrations in the pattern of facial nerve branches (47.6%). Thyroglossal cyst and non-recurrent laryngeal nerves were the next common anomalies noted (14.2%). Preoperative suspicion and diagnosis were evident in three patients. Conclusion: Though rare, congenital anomalies may pose significant challenges to the surgeon. Since most of them are noticed intraoperatively, a thorough knowledge of anatomy and its variation will help prevent injury to these structures. When promptly recognized and appropriately dealt, congenital anomalies do not produce surgical morbidity.