Recent experimental studies of the processing of organic matter in marine sediments by benthic fauna have used isotopically labelled organic substrates as tracers for natural organic matter and have followed processes such as ingestion, bioturbation, remineralisation and burial. In order to use these labelling techniques to trace organic matter on a detailed level through the process of digestion and assimilation, it is necessary to be able to detect isotopically labelled biochemicals and to distinguish them from their natural, unlabelled counterparts. In this study existing methods for the GC analysis of amino acids and aldoses are combined with the Sun-type isotope calibration technique for GC-MS (Sun M. Y., 2000, Org. Geochem. 31, 199-209) to achieve quantitative measurement of 13C labelled amino acids and aldoses in fauna and sediment samples from a feeding experiment. In order to demonstrate the methods, example data from feeding experiments are presented, which suggest that assimilation of amino acids and aldoses by polychaetes during digestion is selective and taxon specific.