Autonomic failure is a prominent clinical feature of patients with multiple system atrophy (MSA). Neurohormonal dysfunction is also a frequent accompaniment in patients with MSA. The determination of the pathological involvement of the autonomic neurons, which are responsible for circadian rhythms and responses to stress, provides new insight into autonomic failure and neurohormonal dysfunction in MSA. The disruptions of circadian rhythms and responses to stress may underlie the impairment of homeostatic integration responsible for cardiovascular and respiratory failures. These notions lead to the hypothesis that a pathological involvement of autonomic neurons is a significant factor of the poor prognosis of MSA. Beyond this perspective, endeavors to find the morphological phenotype that represents a predominant loss of autonomic neurons may elucidate the full spectrum of pathological involvements in MSA.