N-methyl-D-aspartate (NMDA) receptor-evoked excitotoxicity contributes to region-specific loss of glutamatergic synapses responsible for cognitive decline in Alzheimer's disease (AD). Here, the post-synaptic scaffold proteins PSD-95 and SAP-102, which regulate NMDA receptor synaptic activity and expression, were investigated in human AD autopsy brain tissue. Using absolute quantification real-time PCR, we detected reduced expression of synaptophysin in both the pathologically susceptible inferior temporal cortex and hippocampus, consistent with previous reports. PSD-95 and SAP-102 mRNA was reduced, albeit not significantly. Proteins were precisely quantified against recombinant truncated protein standards. No differences were observed for proteins in AD spared occipital cortex between AD cases and controls. PSD-95 and SAP-102 protein expression was markedly reduced in the AD inferior temporal cortex. Both mRNA and protein levels were reduced according to disease severity. SAP102 protein levels were significantly reduced in AD subjects carrying a copy of the APOEε4 allele. This is the first study to investigate SAP-102 in the aging human brain and suggest a possible mechanism for NMDA receptor expression aberrations in AD.