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Currently, archaeologists perform excavations determined by previous geophysical studies to accurately establish the prospective targets and minimize site disturbance. Among others, one of the methods most widely employed is the Electrical Resistivity Tomography (ERT-2D, -3D). However, investigation of the subsoil of archaeological buildings is not possible to carry out with traditional geophysical methods, because the structure itself prevents it. Therefore, it is necessary to design non-invasive special arrays capable of characterizing the subsoil of such buildings, while preserving their historical context. Here we show how this procedure combined with sequences of resistivity observations at depth allowed us to detect a low resistivity body beneath the pyramid of El Castillo in Chichen Itza (Mexico). This feature may be associated with a cavity (karst) partially filled with sweet water. On the other hand, a natural cavity was discovered under El Osario pyramid (south of El Castillo), at the end of the 19th century. Therefore, this pyramid was also studied to validate the effectiveness of this methodology, obtaining outstanding results. This method provides an interesting procedure to investigate the subsoil of archaeological structures for unveiling evidences that allow specialists to understand the religious meaning of these temples. [ABSTRACT FROM AUTHOR]