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The basal forebrain cholinergic system (BFCS) is the major source of acetylcholine for the cerebral cortex in humans. The aim was to analyze the pattern of BFCS and cortical atrophy in MCI patients to find evidence for a parallel atrophy along corticotopic organization of BFCS projections. BFCS volume and cortical thickness were analyzed using high-definition 3D structural magnetic resonance imaging data from 1.5-T and 3.0-T scanners of 64 MCI individuals and 62 cognitively healthy elderly controls from the European DTI study in dementia. BFCS volume reduction was correlated with thinning of cortical areas with known BFCS projections, such as Ch2 and parahippocampal gyrus in the MCI group, but not in the control group. Additionally, we found correlations between BFCS and cortex atrophy beyond the known corticotopic projections, such as between Ch4p and the cingulate gyrus. BFCS volume reduction was associated with regional thinning of cortical areas that included, but was not restricted to, the pattern of corticotopic projections of the BFCS as derived from animal studies. Our in vivo results may indicate the existence of more extended projections from the BFCS to the cerebral cortex in humans than that known from prior studies with animals.