Atherosclerosis is a progressive inflammatory thickening of the arterial wall resulting from increased cellularity and the accumulation of lipids, cellular debris, and extracellular matrix. Conventional determinations of plasma lipoproteins have resulted in a wealth of clinical data documenting the correlation between low- and high-density lipoproteins (LDL and HDL) and cardiovascular disease (CVD) risk. Current mass spectrometry methodologies allow the detection and quantification of multiple molecular lipid species with various structural and functional roles. The opportunities provided by lipidomics for lipid-based biomarker discovery are prominent in disease diagnostics, monitoring of drug efficacy, and translational model development. For example, the analysis of human plasma samples assessing the effects of statins has shown correlative effects between the LDL/HDL ratio and sphingomyelin and phosphatidylcholine. Additionally, at the vascular tissue level, lipids from different classes are enriched in human plaques of coronary arteries and in the aortas of apolipoprotein E-deficient mice exposed to cigarette smoke, highlighting a set of lipid biomarkers for translational research. Molecular lipidomics will provide insights which other lipids may play important roles in vascular disease progression and will serve as novel markers for preventive as well as therapeutic purposes.