Background: The human homologue of the Drosophila discs large tumour suppressor protein (hDLG) and closely related proteins such as postsynaptic density protein 95 kDa (PSD‐95) are associated with N‐methyl‐d‐aspartate receptors (NMDA‐R) and Shaker‐type K+ channels, and are thought to be involved in their clustering. Results: We have identified a protein named DAP‐1 that binds to the guanylate kinase‐like domains of hDLG and PSD‐95. DAP‐1 was found to associate with hDLG, PSD‐95, NMDA‐R and adenomatous polyposis coli protein (APC). Furthermore, we found that DAP‐1 is specifically expressed in the brain and colocalizes with PSD‐95 and APC in mouse cerebellum. We also found that DAP‐1 is colocalized with PSD‐95 and NMDA‐R at the synapses in cultured rat hippocampal neurons. Conclusion: Our findings suggest that DAP‐1 may play several roles in the molecular organization of synapses and neuronal cell signalling by interacting with hDLG and PSD‐95, which in turn are associated with receptors, ion channels and APC.