This paper gives an overview of the ecosystem model APECOSM (Apex Predators ECOSystem Model) which is developed in the framework of the GLOBEC-CLIOTOP Programme. APECOSM represents the flow of energy through the ecosystem with a size-resolved structure in both space and time. The uptake and use of energy for growth, maintenance and reproduction by the organisms are modelled according to the DEB (dynamic energy budget) theory (Kooijmann, 2000) and the size-structured nature of predation is explicit. The pelagic community is divided into epipelagic and mesopelagic groups, the latter being subdivided into vertically migrant and non-migrant species. The model is mass-conservative. Energy is provided as the basis of the model through primary production and transferred through 3D spatially explicit size-spectra. Focus species (tunas at present, but any predator species can be considered) are “extracted” from the global size-spectra without losing mass balance and represented with more physiological and behavioural details. The forcing effects of temperature, currents, light, oxygen, primary production and fishing are explicitly taken into account.