Radioautography of [(3)H]GABA accumulation and immunocytochemistry of glutamate decarboxylase have been used to study anatomically and morphologically the GABA system of the rat habenular (Hb) complex. Radioautographic visualisation of GABA specific neurons show a very high innervation of the complex including both stria medullaris (SM), the habenular commissure and the periventricular thalamic fibers (FPVT). A massive labeled fiber system in the SM appears to divide into two branches when it reaches the Hb nuclei: a part of fibers continue their course dorsally to the nuclei up to the habenular commissure; other fibers enter the Hb lateralis or run along the ventral Hb medialis at the level of FPVT. The staining is markedly diminished in the entire complex in response to SM lesions. In the Hb lateralis, the radioautographic-positive reaction is mainly bound to labeled fibers or axonal varicosities. However GAD immunocytochemistry reveals some GAD-positive cell bodies in the ventro-median portion of the nucleus. In the Hb medialis the radioautographic and immunocytochemical staining is observed in the neuropile between the unlabeled large cell bodies. In the subependymal layer bundles of processes are strongly labeled and form a continual strain behind the unlabeled ependymocytes. Three types of reactive terminals have been differentiated based on size and shape of vesicles. Some of them are exclusively characterized by clear round vesicles and probably have their origin in the septum. Others contain clear vesicles and some large dense-cored vesicles and disappear after mesencephalic Raphe lesions or 5,7-dihydroxytryptamine treatment. They could correspond to terminals of raphe neurons with a double potentiality GABA and 5HT. The last exhibit mainly a dense population of large dark-cored granules similar to the ones found in neurosecretory nerve endings. However numerous fibers morphologically similar to the reactive fibers are unlabeled.