Introduction: Maternal thyroid disease is considered as a risk factor for abnormal thyroid function at birth as well as for long-term morbidity in offspring. The potential harmful effects on the neonate had led to the clinical practice of thyroid function assessment in infants born to mothers with thyroid disease during pregnancy. We evaluated the usefulness of routine thyroid function tests for every newborn of a mother with thyroid dysfunction. Methods: Data were collected retrospectively from the medical files of mothers diagnosed with thyroid disease and their infants (496 mother–neonate pairs). All mothers with diagnosed thyroid disease who gave birth in the years 2016–2019 at our medical center were included. Results: Hypothyroidism was the most common maternal diagnosis (91.4%), among which 48.7% had Hashimoto's thyroiditis. Hyperthyroidism was diagnosed in 8.6% of the cohort; 71.6% of them with Graves' disease. None of the newborns was diagnosed with congenital hypothyroidism in the screening program. Thyroid-stimulating hormone was >10 mIU/l in 14.6% and >20 mUI/l in 2.2%; all had free thyroxine within normal range. Serum thyroid function test identified four infants with thyroid disease: two had congenital hypothyroidism not related to maternal thyroid disease, one had transient familial congenital hypothyroidism and one had neonatal Graves' disease. Conclusions: Thyroid function testing for all newborns of mothers with thyroid dysfunction seems redundant. However, in cases of congenital hypothyroidism in siblings, thyroid function test, in addition to newborn thyroid screening, is recommended and more careful follow-up is indicated. In maternal Graves' disease, thyroid function test on day 2–3 of life is recommended.