The distribution and pharmacological specificity of [3H]tryptamine binding to coronal and horizontal sections of the rat brain were investigated with computer-assisted autoradiography. [3H]Tryptamine bound to brain regions with up to 58% specificity, as determined with 10 microM tryptamine as a displacer. The capacity (Bmax) of saturable [3H]tryptamine binding sites was greatest in the nucleus accumbens and claustrum (660-760 fmol mg protein-1), with intermediate binding site concentrations in hippocampus, septum, olfactory tubercle, frontal cortex, cingulate cortex and caudate-putamen. The phenylalkylamine, p-methoxyphenylpropylamine and the beta-carboline, harmaline, as well as 5-methyl-tryptamine, displaced [3H]tryptamine from each of these brain regions with a potency that approximated the 5-9 nM affinity (Kd) of [3H]tryptamine binding to each site. Only micromolar concentrations of serotonin displaced [3H]tryptamine, which did not bind to S1, S2, D1, D2 or alpha- or beta-adrenergic sites. The unique pharmacology and the regional overlap of [3H]tryptamine binding sites with dopaminergic nerve terminals in the nucleus accumbens and caudate-putamen suggest that tryptamine-containing neurons in the mammalian brain may modulate behavioral functions such as locomotion.