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A robust approach for the determination of frequency dependent complex dielectric permittivity of materials by waveguide measurements is presented. The method is based on a nonlinear system of integral equations related to loaded rectangular waveguide which is solved by the classical iterative Newton method. It is both theoretically and experimentally shown that the method is effective and reliable. The method has no limitations on the geometry of the samples loaded in waveguide, since a 3-D formulation involving the dyadic Green's function is carried out. It is further shown that the method is not so sensitive to the errors or uncertainties on the dimensions of the samples.