In this paper, propagation losses effects present in rectangular waveguide structures are rigorously considered. For this purpose, a new formulation based on the perturbation of the boundary conditions on the metallic walls of the waveguides combined with an Integral-Equation (IE) analysis technique is proposed. Following this advanced technique, the drawbacks of the classical power-loss method are overcome and a complex modal propagation constant is computed. To validate this theory, we have successfully compared our results with numerical data of lossy hollow waveguides. Next, a Computed-Aided-Design (CAD) software package based on such a novel modal analysis tool has been used to predict the propagation losses effects in a 2-pole symmetric bandpass filter.