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Background: The impact of peanut allergy is large and accidental ingestion of peanut can lead to severe reactions. Currently used diagnostic tests, such as skin prick tests (SPT) and determination of specific immunoglobulins (IgE) have, however, limited sensitivity and specificity. Therefore, new tools have to be developed to improve the accuracy of the diagnostic work-up of food-allergic patients. Comprehensive metabolite analysis may provide biomarkers for diagnosing food allergy as metabolite levels reflect actual physiological conditions. We investigated whether metabolites can be found that discriminate between peanut-allergic patients and non-peanut-allergic subjects. Such metabolites may be used for future diagnostic purposes. Methods: Plasma and saliva samples were obtained from 23 participants (12 peanut allergic and 11 peanut tolerant) prior to and after a peanut challenge and measured with 1H nuclear magnetic resonance (NMR) spectroscopy with subsequent multivariate data analysis. Results: Clear differences were observed between NMR spectra of peanut-allergic and peanut-tolerant subjects in plasma as well as saliva. Allergic patients already showed aberrant metabolite levels prior to peanut ingestion, thus before the onset of allergic reactions. Conclusion: This pilot study shows that aberrant metabolite levels as determined by NMR in combination with multivariate statistics may serve as novel biomarkers for food allergy.