Screening for a disease begins a process that should lead to confirmation of the diagnosis, establishment of the etiology, optimal treatment and documentation of outcome. In newborns referred for an elevated thyroid-stimulating hormone (TSH) level on the screening specimen, a detailed family and personal history should be obtained, and a careful clinical examination should be performed. Hypothyroidism should be confirmed by measuring serum TSH and thyroxine (T4) and the underlying etiology established by sodium pertechnetate scintigraphy. Treatment should be started promptly with an adequate dose of levothyroxine. Clinical and biochemical monitoring should be frequent during the first 3 years of life, when the brain can suffer irreversible damage from hypothyroidism. Except in patients with thyroid ectopy or with true athyreosis, permanence of hypothyroidism should be confirmed after 3 years of age by withholding treatment for at least 4 weeks and measuring serum TSH and T4 off therapy. Growth, psychomotor development and school progression should be documented, especially in children from socially disadvantaged families. Transition to adult care is particularly important for females, who should receive counseling about increased levothyroxine needs during future pregnancies. Cognitive outcome has improved dramatically with screening for overt congenital hypothyroidism, but the benefits from treatment of mild isolated hyperthyrotropinemia remain unproven.