Lipid and fatty acid composition are considered to be key parameters that determine the nutritive quality of phytoplankton diets for zooplanktonic herbivores. The fitness, reproduction and physiology of the grazers are influenced by these factors. The trophic transfer of lipids and fatty acids from algal cells has been typically studied by using simple extraction and quantification approaches, which, as we argue here, do not reflect the actual situation in the plankton. We show that cell disruption, as it occurs during a predator's grazing on diatoms can drastically change the lipid and fatty acid content of the food. In some algae, a rapid depletion of polyunsaturated fatty acids (PUFAs) is observed within the first minutes after cell disruption. This fatty acid depletion is directly linked to the production of PUFA-derived polyunsaturated aldehydes (PUA); these are molecules that are thought to be involved in the chemical defence of the algae. PUA-releasing diatoms are even capable of transforming lipids from other sources if these are available in the vicinity of the wounded cells. Fluorescent staining reveals that the enzymes involved in lipid transformation are active in the foregut of copepods, and therefore link the depletion processes directly to food uptake. Incubation experiments with the calanoid copepod Temora longicornis showed that PUFA depletion in PUA-producing diatoms is correlated to reduced hatching success, and can be compensated for by externally added single fatty acids. © 2007 Wiley-VCH Verlag GmbH & Co. KGaA.