An ectopic thyroid located at the base of the tongue is a rare entity, resulting from early developmental defects of thyroid gland embryogenesis during its descent from the foramen caecum to its normal eutopic pretracheal site. This condition is the main cause of congenital primary hypothyroidism, even though signs and symptoms of thyroid dysfunction may also appear later in childhood. Lingual thyroid may sometimes present with symptoms of respiratory obstruction or feeding difficulties. We illustrate the case of a 7-year-old girl with subclinical hypothyroidism due to Hashimoto’s thyroiditis arising in a lingual thyroid. She had never suffered from upper airway obstructive symptoms, but did refer a 3-month history of cough. Rapid normalisation of thyroid-stimulating hormone levels and termination of the cough were attained when the L-thyroxine treatment started. After 6 months a significant reduction of lingual thyroid size was also noted. The diagnostic procedures and therapeutic options in childhood are discussed.