Prior studies reported that the hippocampal volume is smaller in Alzheimer's disease patients carrying the Apolipoprotein E ε4 allele (APOE4) versus patients who are non-carriers of this allele. This effect however has not been detected consistently, possibly because of the regionally-specific involvement of the hippocampal formation in Alzheimer's disease. The aim of this study was to analyze the local effect of APOE4 on hippocampal atrophy in Alzheimer's disease patients. Using high-resolution T1-weighted images we investigated 14 patients heterozygous for the ε4 allele (age 72±8 SD years; MMSE 20±4 SD) and 14 patients not carrying the ε4 allele (age 71±10; MMSE 20±5 SD), and 28 age-, sex-, and education-matched controls (age 71±8; MMSE 29±1 SD). The hippocampal formation was outlined with manual tracing and 3D parametric surface models were created for each subject. Radial atrophy was assessed on the whole hippocampal surface using the UCLA mapping technique. E4 carriers and non-carriers did not differ in their level of impairment in global cognition (p=0.91, Mann-Whitney test) or memory (p>0.29). Hippocampal surface analysis showed the typical pattern of CA1 and subicular tissue atrophy in both ε4-carriers and non-carriers compared with controls (e4 carriers: p<0.0002; ε4 non-carriers: p<0.01, permutation test). The left hippocampal volume was significantly smaller in ε4-carriers than non-carriers (p=0.044, Mann-Whitney test), the effect of APOE4 mapping to the subicular/CA1 region (p=0.041, permutation test). Differences were not statistically significant in the right hippocampus (p>0.20, permutation test). These findings show that hippocampal atrophy is greater in APOE4 carriers in regions typically affected by pathology. APOE4 may affect the structural expression of Alzheimer's disease.