Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease progression and treatment response. A Systems Medicine approach, based on computational models fed with individual patient data, has the potential to provide the basis for a personalised diagnosis and treatment strategy. The PoLiMeR consortium (Polymers in the Liver: Metabolism and Regulation) has identified the inherited, liver-related diseases of glycogen and lipid metabolism as the ideal starting point for innovative research training in personalised ‘Systems Medicine’. Our perspective opens possibilities for the application of novel drugs and diagnostic tools to a range of both rare and frequent diseases. To advance diagnostics and treatment of metabolic diseases beyond the state-of-the art, a new generation of scientists is needed. The complexity of the metabolic network and its aberrant behaviour in disease require experts with a deep knowledge and understanding of Systems Medicine approaches. The lack of truly interdisciplinary researchers, trained in the three ‘pillars of Systems Medicine’ - experimental, computational and clinical research - severely hampers progress in this field. PoLiMeR aims to fill this gap and brings together clinical, academic, and industrial experts on inherited metabolic diseases, computational modelling of the entire human metabolism, organ-on-chip technology, and detailed metabolic profiling. Our mission is to train our Early Stage Researchers (ESRs) to become dedicated Systems-Medicine experts, who can seamlessly collaborate between computational and wet-lab environments, and between clinical, academic, and industrial environments. This training will enable them to become the future leaders in the field and eventually make the difference for the patients.