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Background: The incidence of congenital hypothyroidism (CH) is expected to be elevated in iodine-deficient areas. In this study, the authors aimed to determine the incidence of transient and permanent CH in a large city which is known to be in the zone of moderate iodine deficiency. Methods: Newborn babies in Bursa, Turkey, were screened by measurement of serum thyroid-stimulating hormone (TSH) obtained by heel prick. The babies who had a serum TSH >20 mIU/L were recalled for measurement of T4 and TSH in venous serum. Results: A total of 11 770 newborns were screened over a period of 9 years. The incidence of CH was found to be 1/840. However, after excluding the transient cases, permanent CH was diagnosed in 1/2354. It was impossible to distinguish transient patients from permanent CH by initial laboratory tests (P > 0.05). The estimated power of the study in determining the incidence of CH in the population was 90% (P < 0.05). Conclusion: The authors conclude that the incidence of CH is very high in their population which warrants a country-wide neonatal screening program. Since transient cases cannot be distinguished and untreated transient hypothyroidism may also cause mental retardation, treatment must be started as early as possible with frequent monitoring to optimize the outcome and identify the transient patients.