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Background: Isoflavones present in soybean may contribute to soy atheroprotective effects., Aim of the Study: To investigate the effect of soy isoflavones supplementation on the formation of electronegative LDL (LDL(-)) and its autoantibodies in blood plasma and aortic atheromas of rabbits fed an atherogenic casein-based diet enriched with isoflavones., Methods: New Zealand male rabbits (n = 15) were fed an atherogenic diet (27% casein) supplemented with isoflavones (0.73 or 7.3 mg of isoflavones/kg/day, Low and High Iso groups, respectively) for 180 days. Monthly, blood samples were collected after 12-15 h fasting and at 180 days of treatment all animals were sacrificed. Isoflavones were analyzed in plasma and urine samples by HPLC. LDL(-) in plasma and atheromas was detected by ELISA and immunohistochemistry, respectively, with a monoclonal antibody reactive to LDL(-). Autoantibodies reactive to LDL(-) were analyzed in plasma and aorta by ELISA., Results: Low and High Iso groups had decreased LDL-cholesterol, increased HDL-cholesterol and lower levels of LDL(-) in blood plasma and aortic atherosclerotic lesions than the non-supplemented Control group. IgG autoantibodies reactive to LDL(- )were higher in plasma of the Control group in comparison with the High and Low Iso groups. In contrast, the aortas from animals that consumed isoflavones showed higher levels of IgG reactive to LDL(- )than the Control group., Conclusion: Soy isoflavones showed hypolipidemic effects and decreased the pro-inflammatory LDL(-) subfraction in blood plasma and aorta of hypercholesterolemic rabbits.