From the nucleotide sequences of three cDNA clones of rat brain-specific mRNAs, we deduced the partial amino acid sequences of two previously unknown proteins. We raised antisera to synthetic peptides mimicking short regions of these putative brain-specific proteins, and used these sera in immunocytochemical studies to localize each protein in the brain. One protein is found in large neurons throughout the brain, asymmetrically distributed toward the dendritic pole of the cell cytoplasm, suggesting involvement in the synthesis and/or directional transport of dendritic substances. The sequence of the second protein contains pairs of basic residues similar to precursors for neurotransmitters. The protein is located in (and may be the precursor for the neurotransmitter of) a novel fiber network of major extent with ramifications in cerebellum, hippocampus, and cortex, and in cell bodies in the brain stem, hypothalamus, and caudate nucleus. Our approach provides a direct method for characterizing rare brain molecules which may not have been anticipated and for which there are no known functional assays.