Pendred syndrome and non-syndromic recessive deafness associated with enlarged vestibular aqueduct (NSRD with EVA) are caused by mutations in the SLC26A4 (PDS) gene. Unlike NSRD with EVA, Pendred syndrome is characterized by goiter, which may be present after early adulthood. However, the clinical diagnosis of these two disorders is difficult in deaf children. Expression of the SLC26A4 gene may be responsible for iodide transport in the thyroid as well as for formation and function of the inner ear. Here, we analyzed the SLC26A4 gene and performed thyroid function tests (FT3, FT4, TSH, and Thyroglobulin) on six congenitally deaf infants (mean age 2.7 years) with EVA. Mutation of the SLC26A4 gene was identified in five patients: four were compound heterozygous (H723R/919-2A>G, H723R/IVS15+5G>A, H723R/R581S, IVS7-2A>G/IVS8+1G>A), the fifth had a frameshift mutation (322delC). All the patients demonstrated an elevation of serum thyroglobulin level. FT3 level was elevated in four of the five patients. The patient who did not have a detectable gene mutation showed normal thyroid function. We conclude that the mutations in the SLC26A4 gene identified here are highly associated with high serum thyroglobulin levels in congenital and deafness infants. These mutations may be of value for the diagnosis of Pendred syndrome and NSRD with EVA.