Modified low-density lipoprotein (LDL) is the main source of lipid accumulation in the arterial wall affected by atherosclerosis. We aimed to compare the properties of apolipoprotein B (apoB) from native and modified LDL. Modified (desialylated) LDL and native LDL were extracted from blood of atherosclerotic patients. We characterized apoB structure of LDL particles in total LDL preparation, circulating modified LDL (cmLDL), and native LDL. Intact cmLDL had a twofold lower content of free amino groups than native LDL. Delipidated apoB from cmLDL also had a lower content of free amino groups. The rates of tryptic hydrolysis and elastase digestion of cmLDL were twofold higher in comparison to native LDL. Therefore, cmLDL from atherosclerotic patients had altered apoB properties. Our observations strengthen the hypothesis of multiple modification of LDL in the bloodstream and underscore the importance of desialylated LDL as a possible marker of atherosclerosis.