According to world-wide data obtained from neonatal thyroid screening programs congenital hypothyroidism (CH) occurs with an incidence of 1: 3000 to 1: 4000. Differences of CH-incidence are more likely due to iodine deficiency thyroid disorders or to the type of screening method than to ethnic affiliation. CH is caused by an absent or defective thyroid gland classified into agenesis (22–42%), ectopy (35–42%) and gland in place defects (24–36%). Although a few cases of thyroid dysgenesis have been described as a result of gene mutations, there is no common link to explain the etiological background of the majority of cases. Neonatal screening is severely affected by iodine deficiency leading to an increasing rate of false positive, transient and permanent cases of CH. Despite of low T4 and T3 levels the majority of low-birth-weight infants are not at risk of transient hypothyroidism. Neonatal screening in early discharged neonates mostly is not recommended before day 4. Since the intellectual outcome of CH seems below normal in Germany a CH registry and monitoring program on a national basis is recommended.