The in vitro binding of a new subtype-selective NMDA receptor antagonist, [3H]Ro 25-6981, to rat brain membranes and sections was characterized. The compound bound to a single site on the membranes with a K(D) of 3 nM and a Bmax of 1.6 pmol/mg of protein. Specific binding, defined with a new NR2B-specific antagonist, Ro 04-5595 [1-(4-chlorophenyl)-2-methyl-6-methoxy-7-hydroxy-1,2,3,4-tetrahydroisoqu inoline], at 10 microM, was fully inhibited by several compounds with the following rank order of affinities--Ro 25-6981 > CP-101,606 > Ro 04-5595 = ifenprodil >> eliprodil > haloperidol > spermine > spermidine > MgCl2 > CaCl2--and partially inhibited by competitive glutamate recognition site antagonists. A high density of binding sites was detected, radioautographically, in several layers of the cerebral cortex, in the hippocampus, dentate gyrus, tuberculum olfactorium, caudate putamen, medium densities in the globus pallidus, thalamus, spinal cord dorsal horn, and motoneurons, whereas the cerebellum, pons, and medulla were, with a few exceptions, e.g., locus coeruleus, poorly labeled. Overall, the distribution of [3H]Ro 25-6981 binding sites correlated well with that of NR2B (but not NR2A) transcripts, revealed by in situ hybridization histochemistry. The high affinity of [3H]Ro 25-6981 for NR2B-containing receptors renders this compound the ligand of choice to study the regulation of NR2B-containing receptor expression.