Enrichment of the stable isotopes 13C and 15N across trophic levels is a commonly used tool in studies on organic matter flow and food webs. However, there is still no accepted standard for pre-analysis sample preparation. Thus, potential methodological bias in single studies may hamper comparability and scalability of data from different sources. Sample CaCO 3 content introduces a positive bias in δ13C measurements and a negative bias in δ15N measurements. The acidification of samples to remove inorganic carbonate significantly reduces both δ13C and δ15N. As a standard procedure we recommend (1) acidifying samples with as little hydrochloric acid (HCl) as possible using the drop-by-drop technique, and (2) restraining from rinsing after HCl application. © Inter-Research 2005.