Muography (or muon radiography) is a technique that exploits the penetration capability of muons, elementary particles similar to electrons but with a mass about 200 times larger. High energy muons are naturally produced in the interactions of cosmic rays with the Earth atmosphere. The measurement of their absorption in matter allows the imaging of the inner structure of large bodies. The technological developments in the detection of elementary particles have opened the way to its application in various fields, such as archaeology, studies of geological structures, civil engineering and security issues. We have developed a new approach to the three-dimensional muography of underground structures, capable of directly localising hidden cavities and of reconstructing their shape in space. Our measurements at Mt. Echia, the site of the earliest settlement of the city of Naples in the 8th century BC, have led us to the discovery of a hidden underground cavity, whose existence was not evident with the usual two-dimensional muography graphs. We demonstrate here that our original approach definitely enhances muography discovery potential, especially in case of complex underground systems.