Sample collection procedures of pharmacology and toxicology studies might have a great impact on interpretation of metabolomic study results. Characterization of range variation among sample collection methods is necessary to prevent misinterpretation, as is use of optimal methods in animal experiments to minimize biological/technical variation. Here, we investigated the influence of urine and plasma sample collection and handling procedures on GC-MS based metabolomic studies as follows: for urine, pooling period and tube conditions during collection; for plasma, sampling sites, anesthesia and anticoagulants. Metabolic profiles of urine varied dramatically depending on urine pooling period and tube conditions, underscoring the importance of determining appropriate sampling periods in consideration of diurnal effects and targets of effect/toxicity, and suggesting it would be preferable to keep tubes in metabolic cages under iced conditions for urine sampling. Metabolic profiles of plasma differed depending on blood sampling sites. Anesthesia was not effective in reducing individual variation, although the anesthesia was beneficial in reducing discomfort in rats. In GC-MS based metabolomic studies, we recommend that EDTA be used as anticoagulant in plasma sample preparation, because peaks derived from heparin might overlap with endogenous metabolites, which may induce inter-sample variation. The present study demonstrated that biofluid sample collection and handling procedures provide great impact on metabolic profiles, at the very least for minimizing biological/technical variation, sampling period for urine collection should not be set as a short period, and the use of EDTA is recommended as anticoagulant in preparing plasma for analysis by GC-MS. (C) 2010, The Society for Biotechnology, Japan. All rights reserved.