We examined the localization of fibroblast growth factor-9 (FGF-9) mRNA in the rat brain by in situ hybridization. FGF-9 mRNA was moderately or weakly expressed in widespread regions including the olfactory bulb, caudate putamen, cerebral cortex, hippocampus, thalamus, hypothalamus, midbrain, brainstem and cerebellum. However, FGF-9 mRNA was also strongly expressed in several specific nuclei including the red nucleus and oculomotor nucleus in the midbrain, the vestibular nucleus and facial nucleus in the brainstem and the medial cerebellar nucleus, interposed cerebellar nucleus and lateral cerebellar nucleus in the cerebellum. The cellular localization of FGF-9 mRNA indicated that the mRNA in the rat brain was expressed preferentially in neurons, although FGF-9 was originally isolated from human glioma cells. The localization profile of FGF-9 mRNA is different from those of aFGF, bFGF and FGF-5 mRNAs reported previously. The present findings indicate that FGF-9 has a unique role in the brain.