AbstractA widely used method for the preparation of postsynaptic density (PSD) fractions consists of treatment of synaptosomal membranes with Triton X‐100 and further purification by density gradient centrifugation. In the present study, the purity of this preparation was assessed by electron microscopic analysis. Thin‐section and rotary shadow immuno‐electron microscopy of the Triton X‐100‐derived PSD fraction shows many PSD‐95‐positive structures that resemble in situ PSDs in shape and size. However, the fraction also includes contaminants such as CaMKII clusters, spectrin filaments and neurofilaments. We used magnetic beads coated with an antibody against PSD‐95 to further purify PSD‐95‐containing complexes from the Triton‐derived PSD fraction. Biochemical analysis of the affinity‐purified material shows a substantial reduction in the astrocytic marker glial fibrillary acidic protein and electron microscopic analysis shows mostly individual PSDs attached to magnetic beads. This preparation was used to assess the association of α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionate (AMPA)‐type glutamate receptors with the PSD‐95‐containing complex. AMPA receptors are demonstrated by immunoblotting to be present in the complex, although they do not co‐purify exclusively with PSD‐95, suggesting the existence of two pools of receptors, one associated with the PSD‐95 scaffold and the other not. Of the AMPA receptor‐anchoring proteins tested, SAP‐97 is present in the affinity‐purified preparation whereas GRIP is found only in trace amounts. These results imply that a subpopulation of AMPA receptors is anchored to the PSD‐95‐containing scaffold through interaction of GluR1 with SAP‐97.