The subcellular compartmentalization of brain thyroid stimulating hormone (TSH) in the hypothalamus of the rat was investigated using differential and discontinuous sucrose density gradient centrifugation. When the mitochondrial fraction (P2) was layered on a discontinuous sucrose density gradient (0.32-1.4 M) and centrifuged for 60 min at 72,000 g, TSH recovered from the gradient was found, by double antibody radioimmunoassay, to be associated preferentially with the synaptosomally-rich layers. The separation was monitored by electron microscopic examination of all fractions obtained throughout the procedure. The addition of a large excess of either [125I]-labeled or unlabeled pituitary TSH at the time of homogenization did not influence the amount of immunoreactive TSH associated with the synaptosome-rich fractions, and both the unlabeled and labeled hormone were recoverable in the final supernatant indicating that the simple addition of peptide to hypothalamic homogenates did not result in any preferential association to any particular subcellular fraction. The apparent association of this brain-based pituitary peptide was not, therefore, an artifact of the homogenization process. It is concluded that an association exists between immunoassayable TSH and brain-based synaptosomes in homogenates of the rodent hypothalamus.