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Atherosclerosis can be thought of as a complex process involving many aspects of the patient’s life, ranging from sex, age, and genetics to lifestyle and nutrition. In the last 10 years, there has been a wide expansion of the “-omics” sciences. Such sciences have proven very effective and accurate in the analysis of complex systems, where the analysis of many factors might help a better understanding of the system itself. Among all the “-omics” sciences, metabolomic and metabonomic are gaining increasing interest. Metabonomics quantitatively measures living systems undergoing the effects of diseases. Unlike genomics and proteomics, metabonomics focuses on the multiparameter evaluation of a living complex system by studying its overall physiological profile. Metabonomics can be thought of as a multiparameter profiling technique of each individual.