This work concerns the electrical properties of waveguide applicators consisting of flanged rectangular waveguides filled with a dielectric, used in medical applications (microwave thermography and local hyperthermia). The reflection coefficient and the near field configuration in lossy materials were obtained in some cases analytically and in some other cases numerically. The validity of these methods was verified experimentally. The study shows that the matching of the applicator and the penetration depth in a lossy material, such as a living tissue, depend not only on the tissue characteristics but also on the characteristics of the applicator itself.