The hepatobiliary system and the kidneys are the main routes by which drugs and their metabolites leave the body. Compounds that are mainly excreted into bile in general have relatively high molecular weights, are amphipathic and highly bound to plasma proteins. In contrast, compounds that are predominantly excreted into urine have relatively low molecular weights, are more hydrophilic and generally less protein bound. The first step in drug elimination in liver and kidney is uptake into hepatocytes or into proximal tubular cells. The substrate specificity and affinity of the uptake carriers expressed at the basolateral membranes of hepatocytes and proximal tubular cells could therefore play an important role for the determination of the main elimination route of a compound. This review discusses the tissue distribution, substrate specificity, transport mechanism, and regulation of the members of the organic anion transporting polypeptide (Oatp/OATP) superfamily (solute carrier family SLC21A) and the SLC22A family containing transporters for organic cations (OCTs) and organic anions (OATs). The Oatps/OATPs are mainly important for the hepatic uptake of large amphipathic organic anions, organic cations and uncharged substrates, whereas OCTs and OATs mediate uptake of predominantly small organic cations and anions in liver and kidney.