A great deal of fatigue damage due to severe vibration arises at after ship body, because there are some exciting sources. In order to avoid the resonanse between the ship structure and the exciting forces, it is necessary to estimate exactly the natural frequency of ship structure. The side shell structure of after ship body which recieves directly the propeller surface force is not the flat plate as a general rule, therefore it is not easy to calculate the natural vibration of side shell structure. In this paper, a method to calculate the natural vibration of rectangular and trapezoid shallow shell was presented. And the results by present method were compared to the results by the finite element method. The natural vibration of shallow shell can be fairly good estimated by using the present method, but the magnitude of maximum initial deflection which this method can be applied to is about 20% to the side length. It was also clarified that the plate thickness-maximum initial deflection ratio is one of the parameter which decides the natural frequency of the shallow cylindrical shell. According to the calculated results for the trapezoid shell, in the case that the upper side-lower side ratio c / a is about 0.91.0, the natural frequency is almost equal to that of rectangular shell.