Accurate quantification of synaptic changes is essential for understanding the molecular mechanisms of synaptogenesis, synaptic plasticity, and synaptic toxicity. Here we demonstrate a robust high-content imaging method for the assessment of synaptic changes and apply the method to brain homogenates from an Alzheimer's disease mouse model. Our method uses serial imaging of endogenous fluorescent labeled presynaptic VAMP2 and postsynaptic PSD95 in long-term cultured live primary neurons in 96 well microplates, and uses automatic image analysis to quantify the number of colocalized mature synaptic puncta for the assessment of synaptic changes in live neurons. As a control, we demonstrated that our synaptic puncta assay is at least 10-fold more sensitive to the toxic effects of glutamate than the Mtt assay. Using our assay, we have compared synaptotoxic activities in size-exclusion chromatography fractioned protein samples from 3xTg-AD mouse model brain homogenates. Multiple synaptotoxic activities were found in high and low molecular weight fractions. Amyloid-beta immunodepletion alleviated some but not all of the synaptotoxic activities. Although the biochemical entities responsible for the synaptotoxic activities have yet to be determined, these proof-of-concept results demonstrate that this novel assay may have many potential mechanistic and therapeutic applications. Synapses are asymmetric intercellular junctions that permit neurons to transmit electrical or chemical signals to other neurons. Dysregulated synaptic function, abnormal synaptic plasticity and synaptic loss are involved in many neurodevelopmental and neurodegenerative disorders, in particular Alzheimer's disease (AD) 1-3. As the most common dementing disorder in the elderly, AD is tightly correlated with synaptic loss in vulnerable brain regions, which has led to the hypothesis that loss of synaptic terminals is a key event in early cognitive decline 4. Accurate quantification of mammalian central nervous system synaptic changes is important for understanding the molecular mechanisms of synaptogenesis, synaptic plasticity, and developmental or pathological synapse elimination. As many neurodegenerative conditions are known to affect synapses, quantification of synapses is also critical for identifying synaptotoxic factors and for screening of potential therapeutic agents. However, few efficient methods are available for this purpose. Electrophysiology, electron microscopy, and most light microscopy approaches are costly, time-consuming, and labor-intensive. Unbiased, high throughput screening for synaptotoxic substances in brain disorders such as AD would provide a better understanding of the disease process and an opportunity to identifying new therapeutic targets and drug candidates. High content screening (HCS) combines the efficiency of high-throughput, multi-well plate-based techniques with quantitative image analysis at subcellular resolution 5-7. Recent advances in HCS have made high-throughput analysis of synaptic changes in live neurons po...