Abstract： Objective To identify the diffusion alterations of deep gray matter(GM) and white matter (WM) among Alzheimer's disease (AD), mild cognitive impairment (MCI) and healthy people by atlas?based analysis (ABA), and to investigate the respective relationship with cognitive function. Methods Twenty?one AD patients (AD group), 8 MCI patients (MCI group) and 15 normal controls (control group) were performed by conventional MRI and diffusion tensor imaging (DTI). The raw data of DTI was processed by using DTI studio software to generate the fractional anisotropy (FA) images. Then ABA was used to quantify&nbsp;the FA value in 58 deep GM and WM structures. The differences of FA value among three groups were compared by using one way ANOVA, with a post?hoc analysis. In AD and MCI groups, the partial correlation was further investigated between mini?mental state examination (MMSE) score and FA value in the brain regions that have significant differences between AD and MCI group or between MCI and control group. Results Compared with control group, AD patients showed wide?spread FA decrease in most deep GM and WM regions (corrected P<0.05). The FA values of the hypothalamus, the fornix, the superior longitudinal fasciculus (SLF) and the cingulum in AD group were significantly lower than those in MCI group (corrected P<0.05). The FA value of the right splenium of corpus callosum (SCC) in MCI group was significantly lower than that in control group (MCI:0.550±0.018 vs. Control:0.585±0.026, P<0.05). In AD and MCI group, the FA values of the left hypothalamus, the right hypothalamus, the left cingulum, the right cingulum, and the left SLF were positively correlated with MMSE scores(r=0.502, 0.515, 0.535, 0.527, 0.512; P<0.05). No significant correlation was found between the FA value of the right SCC, the right SLF, the right fornix/stria terminalis, the right fornix and MMSE scores(P>0.05). Conclusion Based on ABA, this study found the diffusion changes not only in the WM but also the deep GM in AD patients, but only WM diffusion disruptions in MCI group. The decreased FA value in the right SCC appeared early, but had no correlation with the cognitive impairment. The FA value in the hypothalamus, the fornix, the SLF and the cingulum decreased with the disease progression, and correlated positively with the cognition decline.