The occurrence of systemic inflammatory response syndrome (SIRS) remains a major problem in intensive care units with high morbidity and mortality. The differentiation between noninfectious and infectious etiologies of this disorder is challenging in routine clinical practice. Many biomarkers have been suggested for this purpose; however, sensitivity and specificity even of high-ranking biomarkers remain insufficient. Recently, metabolic profiling has attracted interest for biomarker discovery. The objective of this study was to identify metabolic biomarkers for differentiation of SIRS/sepsis. A total of 186 meta-bolites comprising six analyte classes were determined in 143 patients (74 SIRS, 69 sepsis) by LC-MS/MS. Two markers (C10:1 and PCaaC32:0) revealed significantly higher concentrations in sepsis. A classification model comprising these markers resulted in 80% and 70% correct classifications in a training set and a test set, respectively.This study demonstrates that acylcarnitines and glycerophosphatidylcholines may be helpful for differentiation of infectious from noninfectious systemic inflammation due to their significantly higher concentration in sepsis patients. Considering the well known pathophysiological relevance of lipid induction by bacterial components, metabolites as identified in this study are promising biomarker candidates in the differential diagnosis of SIRS and sepsis.