It is quite usual to encounter a beam with different types of cross section or even structural discontinuities such as a crack along its length. Furthermore, in many occasions such a beam may happen to be exposed to the oscillatory fluctuations. Therefore, any information about its natural frequencies may be worthwhile. Amongst the problems of discontinues beam analysis, in this paper a special kind of frequency analysis for a cracked and stepped beam located on an elastic foundation is considered. Accordingly, following a look out at the definition of Timoshenko beams, a special modeling trend known as the wave method is introduced. Based on the d' Alembert’s approach for the solution of wave differential equations, the technique of wave method is mainly depended on the study of transmission and reflection of waves colliding to a barrier. The method results in a global frequency matrix, which its determinant gives out the natural frequencies. The wave method is employed for the frequency analysis in some kinds of cracked and stepped beams with different types of boundary conditions. In some typical cases, the results are compared to other similar works and confirmed to be convincing.