BACKGROUND: High-density lipoprotein cholesterol (HDL-C) levels in premenopausal and postmenopausal women are differentially affected by exogenous sex hormones depending on their apolipoprotein E (apo E) genotype. Because endogenous sex hormones markedly increase during pregnancy, we examined whether HDL-C declines after a first birth varied by apo E polymorphisms. METHODS: In 1147 nulliparas (416 black, 731 white), fasting blood samples (nonpregnant) were drawn at baseline and at follow-up years 5, 7, and 10. Time-dependent pregnancy groups included 0 pregnancies (P0), 1+ short pregnancy (P1+), 1 birth (B1), 2 or more births (B2+). ApoE groups by alleles identified with a phenotype method included E4 (4/3 and 4/4), E3 (3/3), and E2 (2/2 and 3/2). Differences in adjusted mean HDL-C changes among pregnancy groups and ApoE groups were examined using repeated measures multiple linear regression. RESULTS: HDL-C declines associated with parity (one or more births) depended on ApoE group (ApoE*Pregnancy Interaction; p < 0.002). For B1 and B2+ vs. P0, HDL-C declines were -2.4 to -2.7 mg/dl in E4 and -3.4 to -4.1 mg/dl in E3. In E2, HDL-C declines were -6.6 mg/dl for one birth, and -11.5 mg/dl for two or more births, each relative to the 0 pregnancies (P0) group (linear trend, p < 0.001). CONCLUSIONS: The degree to which childbearing adversely affects long-term HDL-C declines varies by apo E phenotype, based on a method that accurately classifies genotype. Our findings show that 2/2 and 3/2 genotypes are associated with larger parity-related HDL-C declines than 3/3, 4/3, and 4/4 genotypes.