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The evaluation of the shielding effectiveness (SE) of rectangular metallic enclosures having apertures in their walls and loaded with conducting bodies is the subject of this paper. The conducting objects can be either modifications of the inner part of the enclosure (e.g., simple metal plates or protrusions of the walls) or elements to be protected from external fields (e.g., printed circuit boards or metallic boxes). The SE of such enclosures is thus investigated through an efficient integral formulation based on the method of moments. The proposed approach makes use of a very fast computation of the enclosure Green's functions, based on the Ewald representation and interpolation techniques. The analysis shows that the classical SE of enclosures (calculated when a uniform plane wave impinges on the aperture of an empty enclosure) can be a very tricky figure of merit since the field inside the shield can be seriously affected by the possible presence of 2-D or 3-D conducting loads, especially in the frequency range above the first resonant frequency of the aperture-enclosure system. Comparisons with full-wave results obtained through different commercial software confirm the validity of the proposed technique and its excellent performance.