The amygdaloid complex (AC) was found highly vulnerable to alpha-synuclein (alphaS) pathology in both familial and sporadic Alzheimer disease (AD), and recently, incidental Lewy bodies (LBs) were identified primarily in the lower brainstem. This challenges the traditional view that the substantia nigra (SN) is the region that is predominately affected in the spectrum of LB disorders. We examined the immunoreactivity of alphaS in the SN, the nucleus basalis of Meynert (nbM), and the AC in 904 subjects with or without concomitant AD pathology. AlphaS-positive structures were seen in at least one of the studied brain areas in 121 subjects (13%). The affected regions in the alphaS-positive subjects included the SN (89%), the nbM (73%), and the AC (67%). This study also included 82 sporadic AD patients diagnosed using CERAD criteria. AlphaS-positive structures were seen in 32% of the AD patients, with the SN and AC being equally affected. In a few subjects the AC was the only affected area. However, this was not inevitably associated with AD pathology, but was related to cognitive decline. Incidental LBs in the SN were described in the occasional subjects, with no alphaS pathology in the lower brainstem.