The potential of geophysical methods in the monumental heritage state conservation study is well known. The available geophysical non-destructive techniques can provide important information about the state of preservation of the artefacts without resorting to destructive action. They are extremely useful in identifying unknown or presumed emergencies to better target restoration operations. The advantage of a geophysical survey is that it enables information to be obtained for large volumes of ground that cannot be investigated by direct methods due to cost. Ground-penetrating Radar (GPR) is one of the more used geophysical technique applied in underground exploration. It is a non-destructive methodology that has become a very important tool for the study of the state of degradation of the monumental heritage. GPR is characterised by a wide frequency band ranging from 10 MHz to some GHz and is useful in the localisation of EM discontinuities in the subsurface with high resolution. The paper shows a case history related to the use of the 3D GPR technique to evaluate the state of maintenance of a hypogeum structure located in an urban area. The hypogeum structure was dug in the rock in the medieval period. The structure was used for the transformation of the oil using ancient millstones in stone pushed from mules. It is a structure of great historical value. The hypogeum structure is in danger of falling because of the numerous fractures present in the rock that constitutes the roof of the same structure. The study was made to assist the restoration and valorisation project of the hypogeum. Because of the very narrow thickness of the fractures, special care was needed in the acquisition and processing steps. Although pushed to the limit of the resolution achievable by the available antenna, the study has given quite good results