The distribution of neuropeptide Y (NPY) messenger ribonucleic acid (mRNA) in the rat and mouse brain has been examined. A 28-mer oligonucleotide probe complementary to a distinctive region of NPY mRNA was 3'-end labeled with [35S]-deoxycytosine triphosphate ([35S]-dCTP) by using terminal transferase and was hybridized to fixed sections of rat and mouse brain. The hybridization of the labeled probe to the mRNA in the tissue section was then detected autoradiographically. A strong hybridization signal was seen corresponding to the arcuate nucleus of the hypothalamus. Scattered NPY-mRNA-containing cell bodies were seen throughout the cerebral cortex. Experiments which compared the distribution of NPY mRNA with immunohistochemically detected NPY indicated a similar distribution in the arcuate nucleus of the hypothalamus and cerebral cortex. These results indicate that active transcription of the NPY gene occurs within the brain and this transcription takes place in NPY-containing cell bodies.