Synaptophysin is a synaptic vesicle glycoprotein involved in the regulation process for neurotransmitter release, which is distributed throughout neuroendocrine cells and all neurons in the brain and spinal cord. In an effort to determine whether amyloid β (Aβ)-42 peptides could influence the quantity and biochemical properties of synaptophysin, alterations in the levels of the synaptophysin protein in various soluble fractions were detected in the brains of four genotypes of transgenic mice (Tg) including Non-Tg, neuron-specific enolase (NSE)-hPS2m, NSE-hAPPsw and hAPPsw/hPS2m double Tg mice. Among the four genotypes of Tg mice, the highest levels of Aβ-42 peptides were noted in hAPPsw/hPS2m, followed by NSE-hAPPsw, NSE-hPS2m and Non-Tg mice. In the brains of these mice displaying different levels of Aβ-42 peptides, the levels of soluble synaptophysin were reduced significantly only in the hAPPsw/hPS2m double Tg mice compared to the Non-Tg mice. However, immunohistochemical analysis revealed no differences in the levels of total synaptophysin protein between the neocortex and hippocampus of the four different genotypes of mice. Western blot analysis using four-step fractions with differing solubility revealed a marked decrease in synaptophysin levels in the Tris-buffer saline fraction of hAPPsw/hPS2m double Tg mice and a significant increase in the formic acid fraction, relative to the Non-Tg mice. The results obtained from our in vivo experiments in mice are identical to the results observed in SK-N-MC cells treated with 100 nM Aβ-42 peptides. Therefore, our experiments collectively suggest that Aβ-42 peptides may alter the solubility without changing the total amount of synaptophysin.