This review provides background on the laboratory design for the Multi-Ethnic Study of Atherosclerosis (MESA) as well as the approach used in MESA to select biomarkers for measurement. The research related to the multitude of circulating and urinary biomarkers of inflammation and other novel and emerging biological pathways in MESA is summarized by domain, or pathway, represented by the biomarker. The contributions of MESA biomarkers to our knowledge of these key pathways in the development and progression of atherosclerosis, cardiovascular disease (CVD), diabetes, kidney disease and pulmonary disease are highlighted as are the contributions of MESA to recommendations for clinical use of several of these biomarkers. In addition, contributions of MESA to multi-cohort genomics consortia and current collaborations in trans-omics and metabolomics are noted.