Three urine samples from two prolidase-deficient patients were analysed using 1H NMR spectroscopy. One-dimensional 1H NMR spectra showed a characteristic pattern of overlapping resonances of the proline and hydroxyproline protons of the imidodipeptides. The model compounds Ala-Pro, Gly-Pro, Phe-Pro, Leu-Pro, Val-Pro, Gly-Hyp and Pro-Hyp were measured as well. The non-proline resonances of Val-Pro, Ala-Pro and Gly-Pro could be assigned in the urine spectra. These resonances could then be used for quantification of the corresponding imidodipeptids. The presence of Leu-Pro in the patients' urine was demonstrated by the results of COSY experiments. However, this imidodipeptide could not be quantified owing to overlap of the resonaces in the one-dimensional 1H NMR spectrum of the patients' urine. Phe-Pro, Pro-Hyp and Gly-Hyp could not be assigned in the spectrum of the patient's urine. The characteristic resonances in the urine from a prolidase-deficient patient, i.e. Ala-Pro, Val-Pro, Gly-Pro, and resonances of the (hydroxy)proline part of the imidodipeptides can be used to diagnose this disease.