This paper investigates wave loads of ships that suffer sinkage due to flood in a compartment caused by damage on the side of the hull. By analyzing ships with various sizesof damage opening, the influence of opening size on ship response is investigated. The motion of the damaged ship is analyzed by using the boundary element method, based on three-dimensional potential theory, considering hydrodynamic pressure in the flooded compartments. The shear forces, bending moments and torsional moments are calculated by the direct integration of the three dimensional hydrodynamic pressure on the outer and inner hulls. A RORO passenger ship with length of 174.8 m is considered in the numerical example, and results for wave loads are discussed.