A role for thyroid hormones in the regulation of the rhythmic expression of circadian clock genes is suggested by the finding that surgical removal of the thyroid gland alters circadian behavioral and endocrine rhythms in rodents. Virtually nothing is known about the role of thyroid hormones in the regulation of clock genes responsible for the generation of circadian rhythmicity. To study this issue, we assessed in rats the effect of thyroidectomy/parathyrodectomy (TPX) on the expression of the clock protein, PER2, in the suprachiasmatic nucleus (SCN), the master circadian clock, and in a number of key limbic forebrain structures, the oval nucleus of the bed nucleus of the stria terminalis (BNSTov), the central nucleus of the amygdala (CEA), the basolateral amygdala (BLA) and the dentate gyrus (DG). TPX significantly altered the normal daily pattern of PER2 expression in the BNSTov and CEA, but had no effect on PER2 expression in the SCN, BLA and DG. Thus, although thyroid hormones modulate PER2 expression in the brain, the effect is tissue specific and therefore likely not to be mediated by a direct effect of the hormone on gene expression.