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An iterative technique for the reconstruction of longitudinally inhomogeneous lossy dielectric material loaded in a uniform metallic waveguide is addressed in this paper. The problem is first formulated as an inverse scattering one based on an integral equation in terms of the unknown complex permittivity. By using knowledge of scattering parameters, the Gauss-Newton technique is employed to solve the inverse problem with both the Tikhonov regularization and multiplicative regularization. In order to show the effectiveness of the method, it is tested against numerical and experimental data at X- and K-bands and satisfactory reconstructions are obtained. Experimental results show that the inverse algorithm with multiplicative regularization can be used for the characterization of multilayered structures in a waveguide without needing a priori information.