The aim of this study was to investigate the antioxidant activity of magnoflorine, an alkaloid isolated from Coptidis Rhizoma, against the oxidation of native low density lipoprotein (LDL) and modified LDL. Magnoflorine was found to inhibit the copper-mediated (Cu2+) oxidation of LDL, as well as of glycated and glycoxidated LDL by increasing the lag time of conjugated diene formation and preventing the generation of thiobarbituric acid reactive substances (TBARS). In addition, the results from the fluorescence emission spectra of tryptophan (Trp) supported that the antioxidant activity of magnoflorine could be associated with the protective effect on the structural modification of apolipoprotein B (apoB) required for LDL oxidation. These results suggest that magnoflorine may be useful for preventing the oxidation of various LDL forms.