Congenital hypothyroidism (CH) is detected at a rate of 1 in 3,000 to 4,000 live births, making it the most common congenital endocrine disorder worldwide. CH is most commonly caused by defects in thyroid development leading to thyroid dysgenesis or dyshormonogenesis. Congenital hypothyroidism is usually sporadic, but up to 2% of cases of thyroid dysgenesis are familial, and CH caused by organification defects is often inherited in a recessive manner. The candidate genes associated with this genetically heterogeneous disorder fall into two main groups: those causing thyroid gland dysgenesis and those causing dyshormonogenesis. Genes associated with thyroid gland dysgenesis include the TSHR gene in nonsyndromic CH, and Gsa and the thyroid transcription factor (TTF-1, TTF-2, and Pax-8) genes, which are associated with different complex syndromes that include CH. Among genes associated with dyshormonogenesis, the TPO and TG genes were initially described, and more recently PDS, NIS, and THOX2 gene defects. There is some evidence for a third group of CH conditions associated with iodothyronine transporter defects that are, in turn, associated with severe neurological sequelae.