Milk and dairy foods are naturally rich sources of a wide range of nutrients, and when consumed according to recommended intakes contribute essential nutrients across all stages of the life cycle. Since then, seminal studies recommendations with respect to intake of saturated fat have been consistent and clear; limit total fat intake to 30% or less total dietary energy, with a specific recommendation for intake of saturated fat to less than 10% of total dietary energy. However, recent work has re-opened the debate on intake of saturated fat in particular, with suggestions that recommended intakes be considered not at a total fat intake within the diet, but at a food specific level. A large body of evidence exists examining the impact of dairy consumption on markers of metabolic health, both at a total dairy intake and also at a food level, with mixed findings to date, but suggests that the impact of saturated fat intake on health differs both across food groups and even between foods within the same good group such as dairy. Milk and dairy foods contain a range of nutrients and bioactive components in different levels, housed within very different food structures. The interaction of the overall food structure and the nutrients describes the concept of the ‘food matrix effect’ which has been well documented for dairy foods. Studies show that nutrients from different dairy food sources can have different effects on health and for this reason, they should be considered individually rather than grouped as a single food category in epidemiological research. This review examines the current evidence from randomised controlled trials and meta-analyses, with respect to dairy, milk, yoghurt and cheese on aspects of metabolic health, and summarises some of the potential mechanisms for these findings.