OBJECTIVE To investigate the genetic causes of deaf patients in a special educational school of Chifeng city, Inner Mongolia by SLC26A4 whole gene sequencing. This study focused on analyzing mutations of coding sequence of SLC26A4 gene and their relevant phenotype. METHODS DNA were extracted from peripheral blood of 134 deaf patients of Chifeng special educational school and 100 normal hearing controls in Northern China. SLC26A4 gene mutation was analyzed by direct sequencing for its 20 coding exons. All individuals found with SLC26A4 mutation were given temporal bone CT scan, and those with confirmed enlarged vestibular aqueduct and/or other malformation of inner ear were then given further ultrasound scan of thyroid and thyroid hormone assays. RESULTS The sequencing results revealed 32 cases carried SLC26A4 mutation. Twenty-nine cases underwent temporal bone CT scan. Twentycases were confirmed to have malformation of inner ear by CT scan (eighteen were EVA, one was EVA and other inner ear malformation and one was Mondini Syndrome). The shape and function of thyroid were confirmed to be normal by ultrasound scan of thyroid and thyroid hormone assays in nineteen of these 20 patients except one who had cystoid change in the right side of thyroid. Twelve types of novel variants of SLC26A4 gene were found. CONCLUSION Byscreening SLC26A4 gene coupled with temporal bone CT scan ,we could determine genetic cause related to this gene up to 14.93 % of deaf patients in special educational school of Chifeng city. SLC26A4 is another common gene besides GJB2 that cause deafness in this area. The discovery of novel variants of SLC26A4 gene makes the mutational and polymorphic spectrum more plentiful in Chinese population.