The authors immunocytochemically identified mesopontine cholinergic and rostral raphe serotonergic neurons in brains obtained at autopsy from four patients with multiple system atrophy (MSA) and four matched controls. There was a severe depletion of cholinergic neurons in the pedunculopontine (20 +/- 2 vs 81 +/- 10 cells/section, p< 0.001) and laterodorsal tegmental nucleus (18 +/- 3 vs 47 +/- 4 cells/section, p < 0.001) in MSA. Whereas there was also depletion of locus ceruleus neurons, there was a striking preservation of rostral raphe neurons in MSA.