Effect of L-thyroxine and carbimazole on brain biogenic amines and amino acids content and circulating levels of thyroid hormones has been investigated in rats. L-thyroxine treatment caused marked elevation of 5-HT, histamine and glutamate along with the decline in the level of GABA whereas administration of carbimazole had a contrary effect on rat hypothalamus. Further, L-thyroxine administration also raised histamine as well as glutamate content and decreased GABA level in thalamic region of the rat brain but carbimazole treatment reduced 5-HT and glutamate content in this area of the rat brain. Similarly, cortical content of 5-HT and histamine also increased following L-thyroxine administration whereas carbimazole treatment lowered 5-HT, histamine and glutamate levels. Simultaneously, there was a considerable rise in the circulating levels of T3and T4in L-thyroxine-treated rats and a marked reduction in their levels in carbimazole-treated rats. There is a positive correlation between these amines and the thyroid hormone level. Thus, the results suggest that L-thyroxine and carbimazole administration cause marked alteration in biogenic amines and amino acids in rat brain, which may have an important role in the functioning of thyroid gland.