We observed significant heterogeneity by menopausal status at baseline, but not by age 55 at diagnosis, for the associations of HDL-C and apo(a) with breast cancer risk, with a significant increase in risk among premenopausal but not postmenopausal women (age- and BMI-adjusted, for a doubling in concentration, HDL-C: HRpre 1.64, 95% CI 1.17–2.30 and HRpost 0.83, 0.51–1.35; P = 0.024; and apo(a): HRpre 2.13, 1.33–3.40) and HRpost 0.83, 0.46–1.51; P = 0.008). This evidence concerns the gene AOPEP and breast cancer.