A detailed and comprehensive assessment of risk is the basis to protect communities and assist decision-making towards the sustainable management of territories. For liquefaction this process implies to simultaneously investigate seismic hazard, susceptibility of the subsoil, vulnerability of structures, economic and social relevance of critical infrastructures and ultimately build a comprehensive multi-level model that considers the interaction among all aspects. Developing a methodology to achieve this goal is the scope of Liquefact, a EU H2020 project. A case study pervasively affected by liquefaction damages is here studied as a real scale scenario to identify the main factors of uncertainty. The available data concerning seismic motion, subsoil and building characteristics, damage and economic loss are used to develop a methodology aimed at quantifying and reducing uncertainties in the spatial distribution of risk.