The pathological hallmark of multiple system atrophy (MSA) is fibrillary aggregates of α-synuclein (α-Syn) in the cytoplasm and nucleus of both oligodendrocytes and neurons. In neurons, α-Syn localizes to the cytosolic and membrane compartments, including the synaptic vesicles, mitochondria, and endoplasmic reticulum (ER). α-Syn binds to vesicle-associated membrane protein-binding protein B (VAPB) in the ER membrane. Overexpression of wild-type and familial Parkinson's disease mutant α-Syn perturbs the association between the ER and mitochondria, leading to ER stress and ultimately neurodegeneration. We examined brains from MSA patients (n = 7) and control subjects (n = 5) using immunohistochemistry and immunoelectron microscopy with antibodies against VAPB and phosphorylated α-Syn. In controls, the cytoplasm of neurons and glial cells was positive for VAPB, whereas in MSA lesions VAPB immunoreactivity was decreased. The proportion of VAPB-negative neurons in the pontine nucleus was significantly higher in MSA (13.6%) than in controls (0.6%). The incidence of cytoplasmic inclusions in VAPB-negative neurons was significantly higher (42.2%) than that in VAPB-positive neurons (3.6%); 67.2% of inclusion-bearing oligodendrocytes and 51.1% of inclusion-containing neurons were negative for VAPB. Immunoelectron microscopy revealed that α-Syn and VAPB were localized to granulofilamentous structures in the cytoplasm of oligodendrocytes and neurons. Many vesicular structures labeled with anti-α-Syn were also observed within the granulofilamentous structures in the cytoplasm and nucleus of both oligodendrocytes and neurons. These findings suggest that, in MSA, reduction of VAPB is involved in the disease process and that vesicular structures are associated with inclusion formation.