We have newly established a sensitive, two-site enzyme immunoassay system for neurotrophin-4 (NT-4) and investigated its tissue distribution in the rat nervous system. The minimal limit of detection of the assay is 0.3 pg/0.2 mL of assay mixture. Concentrations of NT-4 were found to be extremely low in all brain regions, irrespective of the animal age, the highest level being found in the brain stem of 40-day-old rats, at 0.12 ng/g wet weight. NT-4 levels in young adult rats were significantly lower in the thalamus and higher in the olfactory bulb, neocortex, hypothalamus and brain stem than respective levels in 1-week-old rats. NT-4 immunoreactivity was strong in large neurons of the red nucleus and pontine reticular nucleus as well as the locus coeruleus, and moderate in cells in the mesencephalic trigeminal nucleus and interstitial nucleus of the medial longitudinal fasciculus. In the rat embryo, stong staining of NT-4 was detected in cells of regions corresponding to the midbrain/pons from E11.5 through E15.5. The intensity was decreased after E13.5 when the cytoplasm of cells in the medulla oblongata, fibers of the cerebellar primordium, and both cells and fibers of the dorsal root ganglion were also stained. Concentrations of NT-4 were detected in regions including the hindbrain and the dorsal root ganglion. Immunoblotting of NT-4-immunoreactive proteins extracted from these two regions revealed a band corresponding to mature NT-4 with a molecular mass of ∼14 kDa. Kainic acid and another glutamte agonist, (+/–)-α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid did not affect NT-4 levels in the hippocampus. The present results show NT-4 to be localized in very limited brain cells and fibers from the embyonic period through to the young adult, suggesting specific roles in brain functions.