PSD-95/SAP90, which binds to the C-terminus of NMDA receptor and Shaker-type potassium channel, is one of the major postsynaptic density proteins. Recently, novel classes of proteins interacting with the guanylate kinase domain of PSD-95 have been identified, guanylate kinase-associated protein (GKAP) and SAP90/PSD-95-associated proteins (SAPAPs). Here we report the isolation of new isoforms of PSD-95 binding protein (GKAP/SAPAP1) using the yeast two-hybrid system. The isolated protein directly interacts with the guanylate kinase domain of PSD-95. Northern blot analyses revealed that the expression of these isoforms containing distinct N-terminal sequences is differentially regulated during brain development. The present findings suggest that each isoform of the PSD-95 binding protein is differentially expressed in a development-dependent manner and may be involved in the complex formation of PSD-95 and channel/receptors at the postsynaptic density.