There are two primary output pathways from the striatum: a projection to the globus pallidus, and projection to the substantia nigra. Certain striatally expressed neuropeptides are differentially distributed between these two pathways. Specifically, enkephalin is expressed in striatopallidal neurons, whereas substance P and dynorphin are expressed in striatonigral neurons. Several serotonin receptors are also prominently expressed in the striatum, but little is known about how they fit into the molecular neuroanatomy described above. We used double-label in situ hybridization to determine the striatal distribution of the mRNAs of the serotonin2A (5-HT2A), serotonin2C (5-HT2C), and serotonin6 (5-HT6) receptors in relation to enkephalin, substance P, and dynorphin expressing output neurons. Rat brain sections were simultaneously hybridized with an 35S riboprobe for one of the serotonin receptors and a digoxygenin labeled riboprobe for one of the neuropeptides. Sections were examined by using brightfield microscopy, and the degree of colocalization of the two mRNAs determined. All the serotonin receptors colocalized extensively with all three of the neuropeptides examined. None of the serotonin receptors showed preferential colocalization in striatopallidal (enkephalin containing), or striatonigral (substance P or dynorphin containing) cells. The 5-HT2A and 5-HT2C mRNAs displayed a differential distribution with regard to the scattered islands of strongly dynorphin mRNA positive cells, which are thought to reside in the striatal patch compartment. Within these islands, 5-HT2C mRNA expression was much higher than in surrounding areas. 5-HT2A mRNA showed the opposite pattern with decreased expression over dynorphin rich cell clusters.