ABSTRACT. The aim of this study was to examine whether the presence of apolipoprotein E epsilon4 (ApoE epsilon4) is associated with a lower bone mineral density (BMD), lower quantitative ultrasound (QUS) measurements, higher bone turnover and fracture risk, and whether these relations are modified by gender and age. A total of 1406 elderly men and women (greater than or equal to 65 years) of the Longitudinal Aging Study Amsterdam (LASA) participated in this study. In all participants, QUS measurements were assessed, as well as serum osteocalcin (OC) and urine deoxypyridinolin (DPD/Cr urine). Follow-up of fractures was done each three months. In a subsample (n = 604), total body bone mineral content (BMC) and BMD of the hip and lumbar spine were measured. In addition, prevalent vertebral deformities were identified on radiographs. In women, the presence of ApoE epsilon4 was associated with significantly lower femoral neck BMD (g/cm(2); mean +/- SEM; epsilon4+, 0.64 +/- 0.01 vs. epsilon4-, 0.67 +/- 0.01; p = 0.04), lower trochanter BMD (g/cm(2); mean +/- SEM; epsilon4+, 0.58 +/- 0.01 vs. epsilon4-, 0.61 +/- 0.01; p = 0.01) and lower total body BMC (g; mean +/- SEM; epsilon4+, 1787 +/- 40.0 vs. epsilon4-, 1863 +/- 23.8; p = 0.04). Women with ApoE epsilon4 also had a higher risk of severe vertebral deformities (OR=2.78; 95%CI: 1.21-6.34). In men, the associations between ApoE status and both hip BMD and QUS depended on age. Only among the younger men (65-69 years) was the presence of ApoE epsilon4 associated with lower BMD values. Bone markers and fractures were not associated with ApoE epsilon4 in either women, or men. In conclusion, this large community-based study confirms the importance of ApoE epsilon4 as a possible genetic risk factor related to BMD and vertebral deformities and demonstrates that its effect is gender related, and depends on age in men only.