Depression and cognitive impairment are both common disorders in elderly people and frequently occur together. Due to the presence of a common set of behavioral and cognitive symptoms, differential diagnosis may become arduous. Neuroimaging may offer a good tool during diagnosis. We performed a coordinate-based meta-analysis to compare gray matter changes in Alzheimer's disease (AD) and late-life depression (LLD). AD and LLD led to brain atrophy in networks only partially overlapping. Both conditions are linked to a reduction of the bilateral hippocampal volume, but AD is correlated with great atrophy in the left anterior hippocampus and bilateral posterior cingulate cortex, while LLD is correlated with great atrophy in the precuneus, superior frontal gyrus, and ventromedial frontal cortex. Present results shed some light on neural underpinnings of AD and LLD and provide new useful evidence for differential diagnosis.