Introduction: The APOE ϵ4 allele predisposes to high cholesterol and increases the risk for lifestyle-related diseases such as Alzheimer's disease and cardiovascular diseases (CVDs). The aim of this study was to analyse interrelationships of APOE genotypes with lipid metabolism and lifestyle factors in middle-aged Finns among whom the CVD risk factors are common. Methods: Participants (n = 211) were analysed for APOE ϵ genotypes, physiological parameters, and health- and diet-related plasma markers. Lifestyle choices were determined by a questionnaire. Results: APOE genotypes ϵ3/ϵ4 and ϵ4/ϵ4 (ϵ4 group) represented 34.1% of the participants. Genotype ϵ3/ϵ3 (ϵ3 group) frequency was 54.5%. Carriers of ϵ2 (ϵ2 group; ϵ2/ϵ2, ϵ2/ϵ3 and ϵ2/ϵ4) represented 11.4%; 1.9% were of the genotype ϵ2/ϵ4. LDL and total cholesterol levels were lower (p < 0.05) in the ϵ2 carriers than in the ϵ3 or ϵ4 groups, while the ϵ3 and ϵ4 groups did not differ. Proportions of plasma saturated fatty acids (SFAs) were higher (p < 0.01), and omega-6 fatty acids lower (p = 0.01) in the ϵ2 carriers compared with the ϵ4 group. The ϵ2 carriers had a higher (p < 0.05) percentage of 22:4n-6 and 22:5n-6 and a lower (p < 0.05) percentage of 24:5n-3 and 24:6n-3 than individuals without the ϵ2 allele. Conclusions: The plasma fatty-acid profiles in the ϵ2 group were characterized by higher SFA and lower omega-6 fatty-acid proportions. Their lower cholesterol values indicated a lower risk for CVD compared with the ϵ4 group. A novel finding was that the ϵ2 carriers had different proportions of 22:4n-6, 22:5n-6, 24:5n-3, and 24:6n-3 than individuals without the ϵ2 allele. The significance of the differences in fatty-acid composition remains to be studied.