Objective: Impaired glucose tolerance (IGT) is one of the presymptomatic states of type 2 diabetes mellitus and requires an oral glucose tolerance test (OGTT) for diagnosis. Our aims were twofold: (i) characterize signatures of small molecules predicting the OGTT response and (ii) identify metabolic subgroups of participants with IGT.Methods: Plasma samples from 827 participants of the Study of Health in Pomerania free of diabetes were measured using mass spectrometry and proton-nuclear magnetic resonance spectroscopy. Linear regression analyses were used to screen for metabolites significantly associated with the OGTT response after 2 hours, adjusting for baseline glucose and insulin levels as well as important confounders. A signature predictive for IGT was established using regularized logistic regression. All cases with IGT (N = 159) were selected and subjected to unsupervised clustering using a k-means approach.Results and Conclusion: In total, 99 metabolites and 22 lipoprotein measures were significantly associated with either 2-hour glucose or 2-hour insulin levels. Those comprised variations in baseline concentrations of branched-chain amino ketoacids, acylcarnitines, lysophospholipids, or phosphatidylcholines, largely confirming previous studies. By the use of these metabolites, subjects with IGT segregated into two distinct groups. Our IGT prediction model combining both clinical and metabolomics traits achieved an area under the curve of 0.84, slightly improving the prediction based on established clinical measures. The present metabolomics approach revealed molecular signatures associated directly to the response of the OGTT and to IGT in line with previous studies. However, clustering of subjects with IGT revealed distinct metabolic signatures of otherwise similar individuals, pointing toward the possibility of metabolomics for patient stratification.