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Among common non-destructive testing techniques, sonic testing is frequently used for the qualitative assessment of historical masonry structures. The present study aims to improve the current capabilities of the sonic test method by exploring: (a) the advantages of automating the inspection; and (b) the use of advanced imaging methods to aid in the interpretation of the results for structural diagnosis. An automated sonic tomography inspection system previously developed by the research team was tested on-site in two remote heritage sites in Albania and Switzerland. The automation of the inspection allowed collecting the large amount of data required for 3D tomographic imaging the interior of different types of masonry walls, which can help detecting and estimating the extension of both poor and sound areas of masonry, as well as inner cracks. Results show the potential of the use of robotic systems for the structural diagnosis of heritage buildings, which can greatly enhance our capabilities of imaging the subsurface of masonry structures.