CVD is the leading cause of death worldwide, and is commonly associated with modifiable risk factors. Most studies to date examining link between food intake and risk of CVD, have focused on modulation of plasma cholesterol concentrations (total cholesterol (TC), LDL-C). However, recent studies suggest LDL particle size is a more sensitive risk marker for CVD with smaller, dense LDL particles reported as more atherogenic than larger, more buoyant LDL. Although dietary guidelines recommend SFA intake of < 10 % of total energy, this does not consider food source, with recent evidence suggesting differing, sometimes beneficial, lipid responses following consumption of SFA from dairy compared to other food sources. This may be from differences in the physical food matrices, the nutrient content of the foods, and/or how these components interact with each other, described as a ‘dairy matrix effect’. Dietary fat not only raises LDL-C, but also HDL cholesterol (HDL-C), associated with reduced CVD risk. HDL particles are complex emulsions of lipids, proteins and microRNAs that exhibit atheroprotective properties. In addition, HDL particles exhibit a very heterogeneous proteomic composition, dependent on a person’s disease state – with a more pro-inflammatory proteome evident in patients with established CVD. This review will discuss the evidence to date on the importance of the food matrix in modulating response to dietary SFA and impact on CVD risk factors. A focus on potential biomarker properties of lipoprotein particles beyond cholesterol and current use of such biomarkers in human nutrition research will be considered.