It is generally considered that iodine deficiency is the single most common cause of preventable mental retardation (MR) and brain damage. The SLC26A4 gene is expressed at the apical surface of thyrocytes and its product forms an efficient iodide-trapping mechanism. To investigate whether variability in the SLC26A4 gene influences the risk of iodine-deficiency based MR, we undertook an association study between SLC26A4 and MR. Participants were recruited from a relatively isolated and traditionally iodine-deficient region with a high prevalence of MR. The SNPs we selected from the dbSNP and HapMap were identified using ARMS-PCR and sequencing methods. Singular-locus and haplotype association analysis indicated no association between the SLC26A4 gene and MR (p>0.05). The negative results suggest that the SLC26A4 gene has no measurable impact on iodine-deficiency based MR. In view of the characteristics of our samples, our study may provide a good reference for research into the transport features of pendrin in the thyrocyte apical surface.