Physicochemical parameters that influence gas chromatographic separation are numerous. Consequently, isotope labelling, because it modifies physicochemical properties, can induce isotopic effects on retention time. Caffeine has been chosen to study this influence because as itself and its metabolites, it allows the preparation of different methylxanthine isotopomers and thus is one of the best models to study isotopic effects induced by stable isotope labelling. Using a caffeine molecule labelled with deuterium at different positions and rat hepatocytes to obtain metabolites, it was possible to study the influence of labelling on retention time [(14% cyanopropylphenyl)methylpolysiloxane] and to point out the role of each labelled site. It appears that isotopic effects induced by the labelling depend not only on the number of labelling atoms but also on whether this labelling is at position 1, 3 or 7 and, consequently, on the role of the labelled site on the function of the molecule.