The metabolic syndrome incorporating obesity, hypertension, dyslipidemia and elevated plasma glucose has reached epidemic proportions leading to an increase in type 2 diabetes (T2D) and cardiovascular disease (CVD). First line treatment for metabolic syndrome is lifestyle intervention (diet and exercise). However, we do not fully understand the effects of diet or exercise on the disease process. Dyslipidemia (raised plasma triglycerides and LDL-cholesterol, and decreased HDL-cholesterol) is an independent risk factor for T2D and CVD. However, these measures do not provide a complete view of the alterations to lipid metabolism associated with these diseases, nor how interventions may influence these processes. Lipidomics presents a new set of tools to address these issues. We have developed a targeted lipidomics platform using liquid chromatography electrospray ionization-tandem mass spectrometry to profile 300–400 lipid species from 10 µL plasma. We have applied this technology to multiple clinical and population based cohorts to define the plasma lipidomic profiles associated with T2D and CVD and to evaluate the potential application of these profiles to assess disease risk. We have performed dietary intervention studies with low fat and full fat dairy foods to characterize the relationship between dairy consumption, lipid metabolism and the risk of cardiometabolic disease. In acute studies differential responses to dairy and soy meals derived through lipidomic analysis of phospholipids (plasmalogens with antioxidant capacity) suggest differences in the metabolism of soybean oil and dairy fat. In a long-term studies, lysophosphatidylcholine, lyso-platelet-activating factor, and several phospholipid fatty acids correlated with full-fat dairy consumption. Lysophosphatidylcholine and lyso-platelet-activating factor were also directly associated with insulin sensitivity and inversely with insulin resistance. These results suggest that both the composition and metabolism of dairy fat may be important factors in cardiometabolic health and disease.