The heat transfer by conduction across a system containing heterogeneities, when subjected to unsteady conditions, is simulated using a boundary element method (BEM), formulated in the frequency domain. The proposed formulation is validated experimentally.In the laboratory tests a steel inclusion was embedded in a confined host medium and unsteady temperatures were applied to its boundary. The thermal properties of the host media tested (molded expanded polystyrene) has been previously defined experimentally. The results showed that the BEM solutions agree well with the experimental results.