During menopause, a sharp increase in cholesterol concentration occurs with an unexplained wide variation in change. Possibly, this is attributable to genetic variation. The authors prospectively studied the effect of the apolipoprotein E (APOE) genotype on the change in cholesterol level with menopause among 1116 Dutch women. Women with the APOE3E3 genotype were regarded as the reference category and changes were adjusted for age at baseline, years of follow-up, years since menopause, and body mass index. At baseline, the women were on average 50.4 years. After 5.9 years of follow-up, the women were on average 4.3 years (S.D. 1.5 years) postmenopausal. The mean increase in cholesterol with menopause in women with the APOE3E3 genotype was 0.67 mmol/L (95% CI, 0.61-0.72 mmol/L). In women with the APOE2E3 genotype the increase in cholesterol was 0.44 mmol/L (CI, 0.32-0.56 mmol/L). The increase in cholesterol in women with the APOE3E4 genotype did not differ from the increase in women with the APOE3E3 genotype. These results show that the increase in cholesterol level with menopause is 30% lower in women with the APOE2E3 genotype when compared with women with the APOE3E3 genotype, indicating that the APOE genotype contributes to the variation in cholesterol increase with menopause.