There is mounting evidence that the consumption of fermented dairy products such as cheese and yoghurt is associated with a reduced risk of type II diabetes. This effect is greater than in fresh milk and differs between cheese and yoghurt. However, the molecular components responsible for the effect are not known. We tested the hypothesis that the lipid and/or glyceride profiles of yoghurts and cheeses are distinct from one another and fresh milk. We developed a novel sample preparation technique for high-fat samples that can be used with Direct Infusion-Mass Spectrometry. We found that the lipid and glyceride profiles of cheddars from the UK, Ireland and France, and hard cheeses from Sweden and Italy were similar to one another but distinct from unfermented dairy products. The lipid and glyceride profile of yoghurts was varied and included types that may be similar to fresh milk. Several odd-chain-containing triglycerides were more abundant, while a variety of others were less abundant, in fermented milk samples. Phosphatidylcholines and phosphatidylethanolamines were more abundant in cheeses, with evidence that the phosphatidylethanomine profile is re-modelled in a way that reflects the bacterial cell envelope. We concluded that a combination of microorganismal metabolism, concentration of the lipid/glyceride fraction and oxidation during fermentation contribute to the observed lipid profile if fermented dairy foods. These differences in the lipid and glyceride profile provide a new avenue for understanding why different fermented dairy foods show a different association with reduced disease risk compared to unfermented dairy.