Congenital hypothyroidism is the most frequent endocrine disorder in neonates. Controversy exists regarding the necessity to adjust current screening programs to also diagnose patients with central hypothyroidism or those with mild forms of congenital hypothyroidism, who have high TSH levels but normal T₄ and normal T₃ levels (also known as 'subclinical hypothyroidism'). Thyroid hormone replacement should start as soon as the diagnosis is confirmed by measurement of elevated TSH and low serum thyroid hormone levels. Further diagnostic approaches, such as ultrasonography, scintigraphy and measurement of thyroglobulin levels, to determine the subtype of congenital hypothyroidism, should not delay initiation of treatment. Recommendations regarding the initial dosage of levothyroxine vary considerably, and no general accepted guideline exists with regards to initial dosage or optimal time point for dose adjustment according to biochemical parameters. More than 30 years after the introduction of the first neonatal screening programs, mental retardation can be prevented in the majority of children (>90%) with congenital hypothyroidism if therapy is commenced within the first 2 weeks of life, making neonate screening for this disorder the most successful population-based screening test in pediatrics.