Association of apolipoprotein E (APOE) ε4 allele with peripheral quantitative computed tomography (pQCT) bone traits at the distal and shaft sites of the radius and tibia was evaluated in the Young Finns Cohort (n=1777). We also analyzed the interactions of the APOE promoter polymorphisms (-219G/T rs405509 and +113G/C rs440446) and bone traits within the APOE ε3/ε3 genotype (n=1025 and n=1013, respectively), and investigated the gene-environment interactions on bone traits with longitudinal saturated fatty acids (SAFA) intake. Differences between the ε4 allele carriers and noncarriers were modest and mostly nonsignificant. Within the APOE promoter -219G/T polymorphism, cortical strength index (CSI) and compressive bone strength index (BSI) at the distal radius (linear, P=0.003 and P=0.05, respectively) and tibia (linear, P=0.01 and P=0.03, respectively), and CSI at the tibial shaft (linear, P=0.04) decreased towards the -219T/T genotype in women. In men, total cross-sectional areas at the radial site and stress-strain index (SSI) at the radial shaft (linear, P=0.03 and P=0.04 and P=0.05, respectively) increased, and conversely cortical bone density and CSI at the radial shaft (linear, P=0.005 and P=0.05, respectively) and CSI at the tibial shaft (linear, P=0.03) decreased towards the -219T/T genotype. In the highest SAFA tertile, women with the -219T/T genotype had the smallest total area and SSI at the radial shaft (P=0.01 and P=0.02, respectively). Subjects with the APOE +113C/C genotype shared similar bone traits as subjects with the APOE -219T/T genotype. In conclusion, APOE genotypes -219T/T and +113C/C could be genetic markers for cortical bone strength. Furthermore, high longitudinal SAFA intake seems to be more detrimental to bone in women with the -219T/T and +133C/C genotypes than others.