In this paper, the problems connected with the time domain simulation of the transient motions of a damaged ship are considered in detail. In particular, the framework, taking into account all the significant degrees of freedom, is based on the assumption of an intact ship to which external forces are considered acting on account of water entering in the compartments, and the stability reduction due to a regular train of waves from arbitrary direction is explicitly considered. The use of a 2D CFD code allows the calculation of the additional forces and moments due to sloshing of the flooding water with free surface. The objective is to develop a system useful since the preliminary design stages, that allows an optimization of the design process in the light of the new, more stringent, IMO rules on stability after damage.