N-methyl-D-aspartate (NMDA) receptors are clustered at synapses via their association with the PSD-95 (post-synaptic density-95) membrane associated guanylate kinase (MAGUK) family of scaffolding proteins. PSD-95 is the best characterized of this family. It is known to associate with NMDA receptor NR2 subunits via a conserved ES(E/D)V amino acid sequence located at their C-termini and thus to promote the clustering, regulation and the trafficking of assembled NR1/NR2 NMDA receptors at synapses. Here we have investigated in more detail NMDA receptor NR2/PSD-95 protein-protein association. Wild-type NR1 and PSD-95alpha were co-expressed with a series of rodent C-terminal truncated constructs of either NR2A or NR2B subunits in human embryonic kidney (HEK) 293 cells and the association of PSD-95alpha with assembled receptors determined by immunoprecipitation. Additional PSD-95 binding domains that differed between NR2A and NR2B subunits were identified. These domains mapped to the amino acid sequences NR2A (1382-1420) and NR2B (1086-1157). These results suggest that NR2A and NR2B may associate with PSD-95 but with different affinities. This may be important in the determination of the lateral mobility of NMDA receptor subtypes in post-synaptic membranes.