Urine contains a clear individual metabolic signature, although embedded within a large daily variability. Given the potential of metabolomics to monitor disease onset from deviations from the "healthy" metabolic state, we have evaluated the effectiveness of a standardized lifestyle in reducing the "metabolic" noise. Urine was collected from 24 (5 men and 19 women) healthy volunteers over a period of 10 days: phase I, days 1-7 in a real-life situation; phase II, days 8-10 in a standardized diet and day 10 plus exercise program. Data on dietary intake and physical activity have been analyzed by a nation-specific software and monitored by published protocols. Urine samples have been analyzed by (1)H NMR followed by multivariate statistics. The individual fingerprint emerged and consolidated with increasing the number of samples and reaches ~100 % cross-validated accuracy for about 40 samples. Diet standardization reduced both the intra-individual and the interindividual variability; the effect was due to a reduction in the dispersion of the concentration values of several metabolites. Under standardized diet, however, the individual phenotype was still clearly visible, indicating that the individual's signature was a strong feature of the metabolome. Consequently, cohort studies designed to investigate the relation of individual metabolic traits and nutrition require multiple samples from each participant even under highly standardized lifestyle conditions in order to exploit the analytical potential of metabolomics. We have established criteria to facilitate design of urine metabolomic studies aimed at monitoring the effects of drugs, lifestyle, dietary supplements, and for accurate determination of signatures of diseases.