In this study, complex permittivity of arbitrarily shaped homogenous materials loaded in different shaped waveguides (rectangular waveguide and circular waveguide) is determined through an iterative inverse algorithm. S-parameters are calculated for chosen material numerically via Method of Moments (MoM), in place of real measurement data for sake of testing algorithm as a first step. Inverse algorithm depends on calculating transmission-reflection coefficients (two port S parameters) with respect to updated complex permittivity, started with an initial guess. At each step, calculated S parameters (either Si) and/or Su) can be used to update complex permittivity in sense of Newton-Raphson numerical approach. Problem is reduced to finding the roots of iterative equation, which is a function of complex permittivity.