The cognitive impairment in patients with Alzheimer’s disease is closely associated with synaptic loss in the neocortex and limbic system. Although the neurotoxic effects of aggregated amyloid‐β oligomers in Alzheimer’s disease have been studied extensively in experimental models, less is known about the characteristics of these aggregates across the spectrum of Alzheimer’s disease. In this study, postmortem frontal cortex samples from controls and patients with Alzheimer’s disease were fractionated and analyzed for levels of oligomers and synaptic proteins. We found that the levels of oligomers correlated with the severity of cognitive impairment (blessed information‐memory‐concentration score and mini‐mental state examination) and with the loss of synaptic markers. Reduced levels of the synaptic vesicle protein, vesicle‐associated membrane protein‐2, and the postsynaptic protein, postsynaptic density‐95, correlated with the levels of oligomers in the various fractions analyzed. The strongest associations were found with amyloid‐β dimers and pentamers. Co‐immunoprecipitation and double‐labeling experiments supported the possibility that amyloid‐β and postsynaptic density‐95 interact at synaptic sites. Similarly, in transgenic mice expressing high levels of neuronal amyloid precursor protein, amyloid‐β co‐immunoprecipitated with postsynaptic density‐95. This was accompanied by a decrease in the levels of the postsynaptic proteins Shank1 and Shank3 in patients with Alzheimer’s disease and in the brains of amyloid precursor protein transgenic mice. In conclusion, this study suggests that the presence of a subpopulation of amyloid‐β oligomers in the brains of patients with Alzheimer’s disease might be related to alterations in selected synaptic proteins and cognitive impairment.