The 5-hydroxytryptamine transporter complex from rat cerebral cortical membranes was solubilized with digitonin. The affinity of the solubilized transporter complex for [3H]paroxetine, a very selective and potent inhibitor of 5-hydroxytryptamine uptake, was not affected and remained unchanged when compared with the parent membrane preparation. The solubilization yield of membrane-bound [3H]paroxetine binding sites was 42%. The pharmacological profile of the solubilized transporter complex was similar to that of the intact transporter in membranes of the cerebral cortex, with the exception of tryptamine, which exhibited a 10-fold loss in potency to inhibit [3H]paroxetine binding to the solubilized transporter when compared to membranes. The Stokes radius determined by gel filtration was 7.6 nm. This successful solubilization of the neuronal 5-hydroxytryptamine transporter complex is the starting point for purification of this macromolecular moiety.