Congenital goiter presenting in the newborn period is very rare. We present a case of primary hypothyroidism presenting as congenital goiter in the newborn period with symptoms in the immediate postnatal life. Hormone replacement therapy was started leading to normal levels of free thyroxine and triiodothyronine. In face of maternal normal thyroid levels, dysharmonogenesis was considered to be the most probable cause of hypothyroidism.