In the present study we have isolated two splice variants of the organic anion transporting polypeptide 3A1 (OATP3A1_v1 and OATP3A1_v2) from human brain. OATP3A1_v2 lacks 18 amino acids at the C-terminal end (692 aa) but is otherwise similar in sequence as OATP3A1_v1 (710 aa). OATP3A1_v1 exhibits a wide tissue distribution with expression in testis, various brain regions, heart, lung, spleen, peripheral blood leucocytes and thyroid gland, whereas OATP3A1-v2 is predominantly expressed in testis and brain. On the cellular and subcellular levels OATP3A1_v1 could be immunolocalized in testicular germ cells, the basolateral plasma membrane of choroid plexus epithelial cells and neuroglial cells of the gray matter of human frontal cortex. Immunolocalization of OATP3A1_v2 included Sertoli cells in testis, in apical and/or subapical membranes in choroid plexus epithelial cells and in neurons (cell bodies and axons) of the gray and white matter of human frontal cortex. The rodent orthologue Oatp3a1 was also widely distributed in rat brain and its localization included somatoneurons as well as astroglial cells. Transport studies in cRNA injected Xenopus laevis oocytes and in stably transfected CHO FlpIn cells revealed a broad substrate specificity for both splice variants. Transported substrates include the prostaglandins E1 and E2, thyroxin and the cyclic oligopeptides BQ-123 (endothelin antagonist) and vasopressin. These studies provide further evidence for the involvement of OATPs in oligopeptide transport. They specifically suggest that OATP3A1 variants might be involved in the regulation of extracellular vasopressin concentration in human brain and, thus, might influence the neuromodulation of neurotransmission by cerebral neuropeptides such as vasopressin.