Congenital hypothyroidism with goiter is a rare disease. In the early neonatal period, the pathology can manifest itself as both hypothyroidism symptoms and signs of tracheal compression with a large goiter. The most common cause of this disease is antithyroid maternal therapy, which accounts for 10-15% of congenital goiter cases. In the case of an unremarkable maternal history, the main cause of goiter is thyroid hormone dyshormonogenesis. Here, we present a case of congenital hypothyroidism with a giant goiter (55 cm3). The child was intubated soon after birth due to respiratory disorders and asphyxia caused by tracheal compression. In addition, the patient had tricuspid valve insufficiency and cardiomegaly. Levothyroxine substitution therapy initiated on the first day of life led to a rapid decrease in the thyroid volume and structural changes in the heart. The patient`s DNA was analyzed using a wide genetic panel «Congenital hypothyroidism»; no mutations were found. Despite the absence of mutations in genes involved in thyroid formation, we consider dyshormonogenesis as the most likely cause of goiter in our patient.