AIMS: To examine the relation between plasma total thyroxine and free thyroxine in children with congenital hypothyroidism. METHODS: Regression analysis was performed on 114 cases on the paired total thyroxine and free thyroxine measurements taken from the same blood sample. Conversion equations were derived using structural relation models. RESULTS: A linear relation was found between log total thyroxine and log free thyroxine values. The regression slopes for values taken before treatment and values taken while patients were receiving replacement treatment were significantly different. CONCLUSIONS: The data suggest that there is a close association between total and free thyroxine in congenital hypothyroidism, but that the relation is changed by thyroid replacement treatment.