In addition to the forms of congenital hypothyroidism caused by dysgenesis of the thyroid gland (agenesia, ectopy), this phenomenon may be caused by enzyme deficiencies of the thyroid hormone synthetic process. These defects, which are hereditary and transmitted as recessive autosomic characters, are clinically manifest in homozygotic subjects in the form of goitres which appears during the neonatal age or, as in more common, during later infancy. At present, mass neonatal screening allows this phenomenon to be diagnosed during the first days of life. The diagnosis of hypothyroidism caused by enzyme deficiency is made on the basis of radioisotopic and ultrasonic studies, and by the assay of plasma levels of thyroglobulin. The exact definition of the specific enzyme activity which is lacking in each case is more complex and has still to be resolved. This study describes the biochemical and pathogenetic characteristics of the different thyroid hormone synthesis defects and includes the findings of previously published diagnosis tests in order to identify the missing enzymatic activity. Lastly, a protocol for the differential diagnosis of the various types of defect is outlined. A specific etiological definition of the altered thyroid metabolism, while providing further insight into the physiopathology of the thyroid and the epidemiology of enzymatic hormone synthesis defects, should not be a motive for delaying the start of substitutive therapy at the earliest possible stage.