A high-performance liquid chromatography (HPLC) method to determine malondialdehyde (MDA) as the 2,4-dinitrophenylhydrazine (DNPH) derivative was applied to biological samples (serum and liver homogenates). Since MDA is considered a presumptive biomarker for lipid peroxidation in live organisms, a model for nutritionally induced oxidative stress (hypercholesterolemic rats) was studied in comparison with normocholesterolemic animals. The effect of diet supplementation with fruits rich in antioxidant polyphenols was assessed. The proposed method showed to be precise and reproducible, as well as sensitive enough to reflect differences in the oxidative status in vivo. A significant decrease of serum and liver MDA concentrations in animals fed diets containing 0.3% of polyphenols from strawberry, cocoa or plum was observed in the normocholesterolemic groups. This reduction was especially noteworthy in the hypercholesterolemic animals, with increased MDA levels indicating enhanced lipid peroxidation in the controls, yet with values parallel to the normocholesterolemic groups in animals fed the polyphenol-rich diets. These results point out the beneficial effects of phenolic antioxidants from fruits in preventing oxidative damage in vivo.