Multiple system atrophy (MSA) is a sporadic neurodegenerative disorder characterized by various combinations of autonomic dysfunction, cerebellar symptoms, parkinsonism, and pyramidal signs. Although MSA is known as a sporadic disease, multiplex families with MSA suggest a genetic predisposition to MSA. The advanced genome research using high-throughput sequencing technology will enable identification of MSA-related genes. Disease-modifying therapy for MSA is expected to be available in the near future. In 2003, the Japan MSA research consortium (JAMSAC) was established to understand the natural history of MSA, which could be the basis for designing clinical trials, and to elucidate the molecular pathogenetic mechanisms of MSA. In Japan, MSA with predominant cerebellar ataxia (MSA-C) is more frequent than that MSA with predominant parkinsonism (MSA-P); this is in contrast to the previous reports from Europe and North America. JAMSAC has conducted a prospective study on the natural history of MSA by using the established consensus criteria for MSA and the unified multiple system atrophy rating scale (UMSARS). Determining the optimum endpoint, sample size, and duration of trial is essential for designing efficient clinical trials. In addition, more sensitive diagnostic criteria are needed to recruit MSA patients in the earlier phase of the condition. Sample size estimation from a longitudinal study suggested the need for sensitive outcome measures, other than UMSARS. Although the knowledge on MSA has increased in the past several decades, biomarkers for this disease are not yet available. The establishment of more sensitive diagnostic criteria and the development of biomarkers are required to conduct more efficient clinical trials for MSA.