The study concluded that these repeats were absent in pathologically confirmed MSA, suggesting an alternative genetic cause. Pathophysiology
Multiple system atrophy can be explained as cell loss and gliosis or a proliferation of astrocytes in damaged areas of the central nervous system. This damage forms a scar which is then termed a glial scar. The presence of inclusion bodies known as Papp–Lantos bodies, in the movement, balance, and autonomic-control centres of the brain are the defining histopathologic hallmark of MSA.The major filamentous component of Papp-Lantos bodies, glial and neuronal cytoplasmic inclusions, is alpha-synuclein. Mutations in this substance may play a role in the disease. The conformation of the alpha-synuclein is different from that of alpha-synuclein in Lewy bodies. The disease probably starts with an oligodendrogliopathy.Tau proteins have been found in some glial cytoplasmic inclusion bodies. Diagnosis
Clinical
Clinical diagnostic criteria were defined in 1998  and updated in 2007. Certain signs and symptoms of MSA also occur with other disorders, such as Parkinsons disease, making the diagnosis more difficult. Radiologic
Both MRI and CT scanning may show a decrease in the size of the cerebellum and pons in those with cerebellar features (MSA-C). The putamen is hypointense on T2-weighted MRI and may show an increased deposition of iron in the Parkinsonian (MSA-P) form.
Histopathological investigation on six cases of pathologically confirmed MSA, using antibodies directed at a variety of α-synuclein epitopes, revealed substantial variation in α-synuclein protein deposition across both cases and brain regions within cases, providing evidence for strains of aggregated conformers that may differentially promote pathological prion-like spread.In 2020, researchers at The University of Texas Health Science Center at Houston concluded that protein misfolding cyclic amplification could be used to distinguish between two progressive neurodegenerative diseases, Parkinson’s disease and multiple system atrophy, being the first process to give an objective diagnosis of Multiple System Atrophy instead of just a differential diagnosis. Classification
MSA is one of several neurodegenerative diseases known as synucleinopathies: they have in common an abnormal accumulation of alpha-synuclein protein in various parts of the brain. Other synucleinopathies include Parkinsons disease, the Lewy body dementias, and other more rare conditions. Old terminology
Historically, many terms were used to refer to this disorder, based on the predominant systems presented. These terms were  discontinued by consensus in 1996 and replaced with MSA and its subtypes, but awareness of these older terms and their definitions is helpful to understanding the relevant literature prior to 1996. These include striatonigral degeneration (SND), olivopontocerebellar atrophy (OPCA), and Shy–Drager syndrome. A table describing the characteristics and modern names of these conditions follows:

Current terminology
The current terminology and diagnostic criteria for the disease were established at a 2007 conference of experts and set forth in a position paper.