Indolamine metabolism in the rat pineal is regulated by central influences mediated through the superior cervical sympathetics. The pineal stalk and medial habenular nucleus also have serotonin-containing cells and an innervation from the superior cervical ganglion (SCG). The present study was carried out to determine if the habenula and pineal stalk are similar to the pineal in certain aspects of indolamine metabolism. No diurnal rhythm in habenular serotonin content was observed, but ganglionectomy or decentralization of SCG results in a significant increase in habenular serotonin content. Unlike the pineal, the habenula and pineal stalk exhibit no rhythm in N-acetyltransferase (N-AT) activity; the activity of the enzyme in those tissues is comparable to low values of the diurnal rhythm in the pineal. N-AT activity in the pineal stalk and habenula is unaffected by sympathectomy. Similarly, there is little, if any, hydroxyindole-O-methyltransferase (HIOMT) activity in the pineal stalk and habenula; unlike the pineal, it is unaffected by continuous environmental lighting conditions or sympathectomy. These observations indicate that neither the pineal stalk nor the habenula represents a ‘deep’ pineal in the rat but that habenular indolamine metabolism is regulated by its peripheral sympathetic innervat