Metabolite concentrations were generally higher in serum, yet still highly correlated between the two matrices. Furthermore, serum revealed more potential biomarkers than plasma when comparing different phenotypes. Altogether, plasma and serum samples from 83 individuals were measured in the same plates. Results showed that metabolite concentrations were generally higher in serum than in plasma. Out of 122 metabolites, 104 were significantly higher in serum and the average value of the relative difference over all metabolites was 11.7% higher in serum. A partial least squares analysis of 377 KORA individuals also demonstrat- ed that plasma samples were clearly separated from serum samples. In addition, we observed an overall high correlation between the values in the two matrices, Doxercalciferol indicating that differences of metabolite concentrations between both matrices are due to systematic changes across all individuals. The present study provides a robust analysis based on a large size sample and highly reliable measurements of metabolites with stringent quality controls. The method has been proven to be in conformance with the FDA-Guideline ‘‘Guidance for Industry – Bioanalytical Method Validation ’’, which implies proof of reproducibility within a given error range. Our results give support of good reproducibility of metabolite measurements in both plasma and serum. Moreover, plasma demonstrates a better reproducibility than serum, which may result from the less complicated collecting procedure for plasma, as it does not require time to coagulate. The large sample size is not only powerful enough to detect metabolite concentration differences between the two matrices but also makes possible the further characterization of the relationship between them. We observed that metabolite concentrations were generally higher in serum and this phenomenon may partly be explained by the volume displacement effect,Diperodon which means that deprotein- ization of serum eliminates the volume fraction of proteins and distributes the remaining small molecular weight constituents in a smaller volume, thus making them more concentrated. Concentration differences in some metabolites were similar to those observed in previous studies and some differences were related to coagulation processes. The higher arginine concentra- tion in serum has been reported before by Teerlink et al.. The release of arginine from platelets during the coagulation process might account for this difference. Our observations that concentrations of some LPCs were higher in serum are consistent with a former study by Aoki et al., who reported increased LPC concentrations, due to release of phospholipases by platelets activated by thrombin, a process that also occurs upon coagulation. Glucose, which represents the majority of hexose, was found in an earlier study to be 5% lower in plasma than in serum. A similar difference was observed for hexose in our measurements. Although the exact reason for this observation is not clear, a shift in fluid from erythrocytes to plasma caused by anticoagulants might play a role. Serum demonstrated a higher sensitivity in biomarker detection. The generally higher metabolite concentrations in serum than in plasma might lead to this advantage. Metabolite measurements in both matrices are subject to a certain level of background noise, which might affect measurement accuracy, especially for metab- olites with low concentrations. Thus plasma is more prone to this effect than serum, where metabolite concentrations are generally higher.