The distribution of cells containing mRNA encoding cholecystokinin was studied in the rat central nervous system by in situ hybridization histochemistry. Cholecystokinin mRNA containing neurons were considerably more numerous than the cholecystokinin-like immunoreactive neurons detected by immunocytochemistry even after colchicine pretreatment and appeared to be heavily, moderately, or lightly labeled. Such neurons were present in the olfactory bulb, olfactory nuclei, layers II-III and V-VI of the cerebral cortex, amygdaloid nuclei, subiculum, hippocampus, claustrum, endopiriform nucleus, several hypothalamic nuclei, most of the thalamic nuclei, ventral tegmental area, substantia nigra, interfascicularis nucleus, linearis rostralis, central gray, Edinger-Westphal nucleus, superior and inferior colliculi, parabrachial nucleus, reticular formation, raphe nuclei, and spinal trigeminal nucleus. This distribution partly confirmed and partly extended the previous immunohistochemical descriptions. Several brain areas such as the thalamus and the colliculi contain cholecystokinin mRNA but are devoid of perikarya exhibiting cholecystokinin-like immunoreactivity. The cerebral cortex and the hippocampus present a far higher density of cholecystokinin mRNA containing cells, including pyramidal neurons, than of perikarya containing cholecystokinin-like immunoreactivity. These results suggest that cholecystokinin or cholecystokinin-related peptides could have a functional role in numerous cerebral pathways including long projections such as cortical or thalamic projections.