In this article, using the wave propagation method, the natural frequencies and mode shapes of an arbitrary non-uniform one-dimensional waveguide are calculated. The non-uniform rods and beams are partitioned into several continuous segments with constant cross-sections, for which there exists an exact analytical solution. At the end of each segment, waves in positive and negative directions are obtained in terms of waves at initial segment and subsequently, the calculations of the mode shapes become simple. By satisfying the boundary conditions, the characteristic equation is obtained and natural frequencies are calculated for both the arbitrary non-uniform rod and beam. Also, by adding waves in positive and negative directions at the end point of each segment, the mode shapes are obtained. To verify the modified wave method presented here, the frequencies and mode shapes of the rod and the beam with a polynomial cross-section having an exact analytical solution are compared and have been proven to be of high accuracy. Besides, comparisons of finite element method are also included. Therefore, this method can also be used to calculate the natural frequencies and mode shapes of rods and beams with any arbitrary variable cross-section for which no analytical solution is available. For the ‘Modified Wave Approach’ developed here, dimensions of transmission matrix remain constant if the number of segments is increased, while in general wave propagation method, dimensions of transmission matrix increase upon increasing the number of segments. Besides this novelty, this method has the advantage that it gives all the natural frequencies and mode shapes, unlike other approximate methods such as weighted residual, Rayleigh–Ritz, and finite difference methods which have their own shortcomings such as limited number of natural frequencies. Also, since each segment has an exact analytical solution, in contrast to other approximate methods, much higher accuracy is obtained even with only a few number of partitions.