Newborn screening for congenital hypothyroidism (CH) has been highly effective in preventing devastating neurodevelopmental and physical sequelae in affected infants. We report a case of an ectopic thyroid gland located in the submandibular area detected at the age of 3 months, which was missed by congenital hypothyroidism screening test based on twice-repeated TSH measurement in dried blood spots. The diagnosis of subclinical hypothyroidism was confirmed on the basis of blood test performed in the endocrine clinic: TSH 26.3 µIU/ml (N: < 10 µIU/ml), with FT4 14.7 pmol/l (N: 10–25 pmol/l) and fT3 6.9 pmol/l (N: 3–8 pmol/l). Ultrasonography and scintigraphy revealed ectopically located thyroid tissue in the sublingual area. In the case of doubtful results of a neonatal screening test or in any case of suspected congenital hypothyroidism, the diagnosis should be supplemented with ultrasound examination of the neonate’s neck and followed by scintigraphy if necessary.