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The characterization and cellular localization of human brain mRNA encoding the serotonin transporter were investigated using northern blot analysis and in situ hybridization histochemistry. In contrast to results from rodent studies, in which single hybridizing mRNAs are detected in brain and periphery, northern analysis of human midbrain raphe tissue revealed the presence of three mRNA species absent from samples prepared from substantia nigra/ventral tegmental area. In situ hybridization studies revealed dense hybridization signal corresponding to serotonin transporter mRNA highly localized to neurons of the dorsal and median raphe nuclei and the caudal linear nucleus. No hybridization signal was observed in neurons of the substantia nigra or locus ceruleus. These findings demonstrate the first anatomical visualization of human brain serotonin transporter gene expression and reveal heterogeneity associated with serotonin transporter transcripts, similar to, but distinct from the pattern of expression visualized in human peripheral tissues.