Lipids are ubiquitous in the human body, playing diverse biochemical and physiological functions. Unfortunately, lipids are susceptible to oxidation in vivo by free radicals. Lipid hydroperoxides (LOOH) are one of the primary products of lipid peroxidation which play a crucial role in the pathogenesis of oxidative stress, inflammation, and atherosclerosis. Understanding the underlying molecular mechanism of these diseases is critically important for risk stratification, prevention, and therapeutic intervention. Despite its importance in the atherosclerotic process, the qualitative and quantitative evaluations of LOOH in the biological samples have been largely limited, because of structural variability, instability and rapid clearance from circulation. Application of liquid chromatography/mass spectrometry (LC/MS) has revolutionized the study of lipidomic and eased the identification and quantification of hundreds of molecular species of oxidized lipids derived from fatty acids, cholesteryl esters, triacylglycerol and phospholipids in various biological samples. In this review, we will be discussing oxidized lipid species in human lipoproteins, its analytical consideration and significance. An overview of lipids and its oxidative products in lipoproteins, technological advances its identification and quantification using mass spectrometry, and its possible linkage to disorders of lipid metabolism will be discussed.