Scope The Mediterranean (MED) diet is considered to be beneficial, however the contribution of the MUFA component in these beneficial effects is unclear. Therefore, we wanted to disentangle the effects of MUFA from the other components in a MED diet. Methods and Results We performed a randomized fully controlled parallel trial to examine the effects of the consumption of a saturated fatty acid (SFA)‐rich diet, a MUFA‐rich diet, or a MED diet for eight weeks on serum metabolome, in 47 subjects at risk of the metabolic syndrome. We assessed 162 serum metabolites before and after the intervention, by using a targeted NMR platform. 52 metabolites were changed during the intervention (FDR p<0.05). Both MUFA and MED diet decreased exactly the same fractions of LDL, including particle number, lipid, phospholipid and free cholesterol fraction (FDR p <0.05). The MED diet additionally decreased the larger subclasses of VLDL, several related VLDL fractions, VLDL‐triglycerides, and serum‐triglycerides (FDR p<0.05). Conclusion Our findings clearly demonstrate that the MUFA component is responsible for reducing several LDL subclasses and fractions, and therefore causes a more anti‐atherogenic lipid profile. Interestingly, consumption of the other components in the MED diet show additional health effects. This trial was registered at clinicaltrials.gov as NCT00405197.