The aim of this study was to investigate whether the effect of apolipoprotein E polymorphism (APOE) on somatic and lipid risk parameters varies in women of differing reproductive status. We analyzed 447 Slovak women aged between 39 and 90 years. APOE genotypes were determined by PCR-RFLP. Regression analysis confirmed the effect of the APOE genotype on the levels of LDL-cholesterol, apolipoprotein B (apoB), nonHDL-cholesterol and on the three atherogenic indices: apoB-to-apoA1, TC-to-HDLcholesterol, LDL-C-to-HDL-cholesterol. Here, lower mean levels were registered in the E2 carriers than in the E3 and E4 subgroups. However, the impact of menopausal status on lipid parameters was not confirmed. Bonferroni correction showed that systolic blood pressure was significantly lower in the E4 carriers compared to the E3 group (P=0.017). Univariate analysis of covariance revealed a significant interaction between the menopausal group and the APOE group, and their common effect on waist-to-hipratio (WHR). Bonferroni correction in early postmenopausal women showed that the mean WHR values were significantly different between E2 and E4 groups (P=0.008). This study demonstrates that the E*2 allele has a protective effect against higher blood lipid levels. Moreover, the results suggest that E*2 could have a partial negative effect on WHR in early postmenopausal Slovak women.