In this paper a specific procedure for the structural assessment of a container stack is implemented to a realistic case in order to evaluate its effectiveness in the prediction of the operational limits of a container vessel. The feasibility of an extensive calculation based on such procedure is tested, paving the way to the direct analysis of a container stack subject to the inertial loads arising from the ship motions. The procedure is based on a 3D non-linear FE analysis coupled with a direct simulation of non-linear ship motions for the determination of inertial forces acting on a container stack. A non-linear approach has been used for modelling both the ship motion response and the container stack structural response, leading to a global large amplitude analysis. A simplified model of a container stack has been defined in order to decrease the computational cost of the structural calculations, allowing for a use in the framework of an extensive analysis considering many different ship sailing conditions. As final results, diagrams showing the occurrence of failure of container structures or lashing equipment are presented.