The adverse effects of obesity support the use of biomarkers to help elucidate disease mechanism, therapeutic interventions, and preventive strategies. Emerging biomarkers for obesity-associated cardiovascular disease (CVD), type 2 diabetes and cancer play diverse roles in biological pathways including immune modulation and fat metabolism. Animal and in vitro data support the association of these biomarkers with obesity-associated diseases, but evidence in humans is still lacking. In humans, plasma levels of biomarkers are widely used to determine risk, but many studies are limited by ethnicity/race, gender or sample size. In this chapter, the use of biomarkers in obesity research and in the context of CVD, type 2 diabetes and cancer will be discussed. Markers of exposure (adipokines), effect (resulting metabolic abnormalities), and susceptibility (genetic determinants for obesity and related disorders) are covered for each of the three diseases.