We describe the pathological findings in two patients who developed atypical parkinsonism and autonomic failure, leading to a diagnosis of multiple system atrophy (MSA). Postmortem examination of the brain showed cell loss restricted to substantia nigra and locus coeruleus. However, glial cytoplasmic inclusions (GCIs) were present in both cases. We propose that GCIs are highly suggestive of a pathological diagnosis of MSA in the absence of detectable cell loss outside pigmented brain stem nuclei and that brains from cases of atypical parkinsonism should routinely be examined for their presence.