First branchial arch syndrome is a congenital disorder characterized by a wide spectrum of anomalies in the first branchial arch, mainly affecting the lower jaw, ear, or mouth, during early embryonic development. We sought to confirm a suspected case of this syndrome by making differential diagnosis and taking an intensive clinical approach. A 12-year-6-month-old girl with a horizontally impacted left canine in the maxilla had the history of digital fusion in her hands and feet and has been suffering from hearing impairment of her left ear. To diagnose this case and make her careful treatment plan, we further carried out cephalometric analysis and mutation analysis. Her face looks like asymmetry and is not apparently symmetric by cephalometric analysis. Mutation analysis of the patient was conducted by direct DNA sequencing of the goosecoid gene, which is an excellent candidate for determination of hemifacial microsomia, but no changes in this gene were identified. We could not precisely diagnose this case as first branchial arch syndrome. However, certain observations in this case, including hearing impairment of the left ear, allow us to suspect this syndrome.