Deficiency of thyroid hormone during central nervous system ontogeny results in a variety of clinical, anatomical and biochemical defects. Delay in thyroxine therapy in newborns with congenital hypothyroidism leads to irreversible brain damage. We have used localized in vivo proton magnetic resonance spectroscopy (MRS) to assess biochemical changes in different regions of brain in three patients with congenital hypothyroidism before and after thyroxine therapy. An abnormal lipid peak which disappeared with thyroxine therapy was observed in cerebellum and frontal lobe in one patient. Statistically significant reduction of NAA/(Cr+PCr) [P<0.009] and elevation of Cho/(Cr+PCr) [P<0.008] ratios in comparison to controls were documented in all three patients which tended to normalise with thyroxine therapy. A variety of biochemical abnormalities relatable to myelin maturation were documented and these were found to be reversible on thyroxine therapy. Reversibility was documented even though thyroxine therapy was initiated at ages beyond which abnormalities in myelinogenesis are considered irreversible. Also, proton MRS revealed biochemical heterogeneity between patients with congenital hypothyroidism. Copyright 1998 Elsevier Science B.V.