Axenfeld-Rieger syndrome (ARS) manifests varying degrees of anterior segment dysgenesis and carries a risk of resistant glaucoma. It can affect ocular and extraocular structures derived from the neural crest. A small part of the thyroid gland originates from the neural crest, and defects in thyroid origination can result in thyroid agenesis. Thyroid agenesis is a cause of congenital hypothyroidism. To the best of our knowledge, no information exists about ARS associated with congenital hypothyroidism caused by congenital agenesis. We have presented clinical features the first case of ARS associated with congenital hypothyroidism.Keywords: Axenfeld-Rieger Syndrome, Anterior Segment Dysgenesis, Congenital Hypothyroidism, Neural Crest, Thyroid Agenesis.