We present a comprehensive comparison of the anatomical distributions of the cloned mu, delta and kappa opioid receptor mRNA in rat brain. Northern blot analysis revealed that mRNA species encoding the three receptors differed in size and were differentially localized in brain regions. In peripheral tissues analyzed, the 3 mRNA species were detected only in the spinal cord. The distributions of mu, delta and kappa receptor mRNA in rat brain were examined by in situ hybridization histochemistry using gene-specific probes. Mu receptor mRNA was predominately localized to thalamic, brainstem and reticular core nuclei and was highest in the habenular and thalamic nuclei. In contrast, kappa receptor mRNA was expressed in hippocampus including dentate gyrus, hypothalamic and some thalamic nuclei and also present in cortex, caudate putamen, olfactory tubercle and nucleus accumbens. Delta receptor mRNA was prominent in cerebral cortex, olfactory tubercle, hippocampus, caudate putamen and nucleus accumbens. These results show that the mRNA distribution for each opioid receptor subtype in brain is unique and correlate well with the known distribution of the corresponding opioid receptor binding sites.