The authors present the first known reported case of hemifacial microsomia associated with a Chiari I malformation and syrinx. A 14-year-old girl presented with progressive torticollis of 3 years' duration and headaches exacerbated by exercise. Computerized tomography scanning and magnetic resonance imaging revealed extensive craniofacial and vertebral abnormalities, including aplasia of the floor of the left middle fossa and posterior fossa cranium, articulation of the left mandibular condyle with the left temporal lobe, and progressive development of a Chiari I malformation with associated syringomyelia. The patient first underwent posterior fossa decompression, duraplasty, and occipitocervical fusion. This procedure was later followed by reconstruction of the floor of the left middle fossa and temporomandibular joint. The patient's outcome was excellent. In this case report the authors review the complex embryological development of craniofacial and craniovertebral structures, and emphasize the use of a staged approach to treat pathophysiological consequences of this congenital anomaly.