Serotonin (5HT) transporters (SERTs) are responsible for clearance of synaptic and plasma 5HT and are molecular targets for multiple therapeutic and addictive compounds. Recently brain and peripheral SERT cDNAs have been cloned and characterized functionally in transfected cells. Antipeptide (S365) and anti-fusion protein (CT-2) antibodies, directed at epitopes poorly conserved among other Na+/Cl- cotransporters, have been prepared to facilitate the identification and characterization of SERT proteins in native and transfected cells. Immunoprecipitations and immunoblots of rat/human SERT-transfected HeLa cells reveal specific SERT-immunoreactive glycoproteins absent from extracts of vector-transfected cells and absent when incubations were conducted using peptide- or fusion protein-absorbed antibody. In SDS-PAGE of membranes prepared from rat midbrain and cortex, SERTs migrate as single 76 kDa polypeptides with a relative abundance consistent with the known distribution of 5HT neurons and axonal projections. SERT-immunoreactive proteins are also detectable in platelet and pulmonary membranes, sites of peripheral 5HT uptake, but not in liver. Our studies also indicate that brain and platelet SERTs are formed from identical polypeptides differing significantly in their extent of N-linked glycosylation. Immunocytochemistry performed on rat brain sections with CT-2 antibody revealed SERT expression associated with brainstem raphe nuclei in a pattern virtually identical to that obtained by labeling adjacent sections with 5HT antisera. SERT-immunoreactive fibers were found to be widely distributed throughout the rodent brain, with highest density in forebrain regions known to receive a dense serotonergic innervation. In a similar manner, CT-2 antibody also detects endogenous expression of human SERT proteins, providing an opportunity for future studies on the modulation of transporter protein expression in neurologic and psychiatric disorders.