Colchicine is selectively neurotoxic towards some neuronal populations and causes the death of sensitive neurons. Electron microscopic examination of the neural damage caused by stereotaxic injections of colchicine has been used to demonstrate neuroanatomical connections in the septohabenulointerpeduncular system of the rat brain. Colchicine injections in the medial habenula were selectively neurotoxic towards some neurons of the medial habenula and resulted in degeneration of S and crest terminals, the most common type of interpeduncular synapses. Control injections in the stria medullaris, rostral to the habenular complex, caused only sparse degeneration in the interpeduncular nucleus and did not involve S and crest terminals. Colchicine injections that caused neuronal degeneration in the supracommissural septum resulted in substantial terminal degeneration in the interpeduncular nucleus. A large number of degenerated terminals was also present, in these cases, in the medial habenula. Colchicine administration in the various areas caused, to a different extent, lesion or minor ultrastructural damage to axons crossing the injected area. The potential usefulness of colchicine neurotoxicity for neuroanatomical purposes is discussed and the limitation derived from damage of fibers of passage is considered. Colchicine can be confidently used in experimental studies only when erroneous interpretation caused by damage of fibers of passage can be excluded. In the present investigation, this prerequisite could be achieved either by controls made possible by the peculiar arrangement of neuronal circuits or by comparison with known anatomical data.