In two laboratory experiments using tilapia (Oreochromis niloticus) and common carp (Cyprinus carpio), we investigated the effect of lipid content in the fish carcass on the stable carbon isotope ratio (δC). In both experiments, a significant negative correlation was found between lipid content in the carcass dry matter and δC of total dry matter, but there was no influence on the δC of fat-free dry matter or lipids. As the lipid content of fish is known to vary with reproductive stage, season or nutritional state, separate analysis of fractions of the proximate composition of dry matter will lead to more reliable results than analysing the whole body. The differences in δC between diet and fish carcass (trophic shift) were different for the two species, calling for feeding trials under controlled conditions using the species and the feeds in question before applying the stable isotope tracer technique in the analysis of food webs.