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Background and purpose: How the APOE genotype can differentially affect cortical and subcortical memory structures in biomarker‐confirmed early‐onset (EOAD) and late‐onset (LOAD) Alzheimer's disease (AD) was assessed. Method: Eighty‐seven cerebrospinal fluid (CSF) biomarker‐confirmed AD patients were classified according to their APOE genotype and age at onset. 28 were EOAD APOE4 carriers (+EOAD), 21 EOAD APOE4 non‐carriers (–EOAD), 23 LOAD APOE4 carriers (+LOAD) and 15 LOAD APOE4 non‐carriers (–LOAD). Grey matter (GM) volume differences were analyzed using voxel‐based morphometry in Papez circuit regions. Multiple regression analyses were performed to determine the relation between GM volume loss and cognition. Results: Significantly more mammillary body atrophy in +EOAD compared to –EOAD is reported. The medial temporal and posterior cingulate cortex showed less GM in +LOAD compared to –LOAD. Medial temporal GM volume loss was also found in +EOAD compared to –LOAD. With an exception for +EOAD, medial temporal GM was strongly associated with episodic memory in the three groups, whilst posterior cingulate cortex GM volume was more related with visuospatial abilities. Visuospatial abilities and episodic memory were also associated with the anterior thalamic nucleus in –LOAD. Conclusions: Our results show that the APOE genotype has a significant effect on GM integrity as a function of age of disease onset. Specifically, whilst LOAD APOE4 genotype is mostly associated with increased medial temporal and parietal atrophy compared to –LOAD, for EOAD APOE4 might have a more specific effect on subcortical (mammillary body) structures. The findings suggest that APOE genotype needs to be taken into account when classifying patients by age at onset. [ABSTRACT FROM AUTHOR]