The ligand preferences of recombinant NR1 homomeric and NR1-NR2 heteromeric NMDA receptors were examined by homogenate binding assay. The binding affinities for most ligands were similar to those reported for native NMDA receptors. The order of affinity for [3H]glutamate was NR1-NR2B > NR1-NR2A approximately NR1-NR2D > NR1-NR2C > NR1. NMDA had approximately equal affinity for all heteromeric types (Ki approximately 5 microM), but the competitive antagonists CGS 19755 (cis-4-(phosphonomethyl)piperidine-2-carboxylic acid) and CGP 39653 (D,L-(E)-2-amino-4-propyl-5-phosphono-3-pentenoic acid) displayed the affinity order NR1-NR2A > NR1-NR2B > NR1-NR2D > NR1-NR2C. Binding of [3H]CGP 39653 could only be detected at the NR1-NR2A receptor type (Kd approximately 6 nM). The glycine site antagonist [3H]5,7-dichlorokynurenate bound with good affinity to all recombinant receptors (Kd approximately 50-100 nM), while glycine exhibited an affinity order of NR1-NR2C >> NR1 = NR1-NR2B = NR1-NR2D > NR1-NR2A. The channel-site ligand [3H]MK 801 ((+)-5-methyl-10,11-dihydro-5H- dibenzo[a,d]cyclo-hepten-5,10-imine hydrogen maleate) showed the affinity ranking NR1-NR2A = NR1-NR2B >> NR1 > NR1-NR2C = NR1-NR2D. Thus the ligand binding affinities of recombinant NMDA receptors is dependent on their subunit composition. The NR1-NR2A, NR1-NR2B, NR1-NR2C and NR1-NR2D receptors may account for the antagonist-preferring, agonist-preferring, cerebellar, and medial thalamic subtypes of native NMDA receptors, respectively.