Since April 2012, genetic testing for congenital hearing loss is covered by the public health insurance in Japan. Recent (since August 2015) developments in next-generation sequencing technology have enabled the detection of 154 mutations in 19 genes. Genetic testing provides valuable information on hearing phenotype, prognosis, and prediction of associated symptoms. We report a hearing-impaired patient in whom multiple genetic mutations were detected. This patient carries two missense mutations in GJB2 (p.G45E, p.Y136X), as well as a mitochondrial mutation (7445A>G). Since the number of genes detectable by genetic testing has increased, the diagnosis of hearing loss can be made with greater accuracy. However, it is often difficult to clinically understand and interpret the genotype information, especially when multiple gene variants are detected in one patient or family. Genetic counseling plays an important part in the intervention for or follow-up of such patients. Genotypic and phenotypic information of other family members is necessary, so that both the patient and the family can understand and accept the results of genetic testing.