This paper deals with general procedure of the direct structural analysis of a container vessel and some difficulties encountered during the application of wave induced loads in real projects. Direct structural analysis requires a design wave representing the most probable extreme wave condition during its lifetime and an appropriate application scheme of wale loads into FE model of a hull. A design wave condition is determined by spectral analysis using the transfer function of a dominant load component, based on a given probability level. Dynamic and static load components are combined to get real condition of a vessel under waves. The effects of wave crest and trough are generated by modification of pressure distribution along the side shell. Counter accelerations are introduced to make the system in a state of equilibrium. FE model of the hull is also adjusted considering the realistic positions of center of gravity. Several idealization schemes are adopted to apply inertia forces induced from the mass of a vessel combined with applied accelerations. Main attention is paid to keep global effects obtained in wave load analysis throughout structural analysis. The results of rigorous application of wave loads into FE model are compared with those of simplified method in which only global effects such as vertical and horizontal bending moment and torsional moment are applied. It is shown that the proposed method gives more reliable results than the other methods, and is useful for practical uses.