The primary objective of this paper is to approach the use of the 3D Geographic Information Systems (3D GIS), as an instrumental tool that allows us to deal efficiently with the extensive amount of information that characterises a large part of the research carried out in the field of Urbanism and Regional Planning. Specifically, the study focuses on medium-sized cities in Andalusia, the most populous and the second largest region in Spain. The Andalusian urban system is substantially characterised by the historical importance of this type of cities within its territorial organisation, which dates back to more than two thousand years, and whose potential as sustainable and balanced stands out. In particular, it is intended to address features related to urban characterisation as medium-sized cities that have been declared as heritage sites, as well as, the integration of the cultural heritage into urban development planning as an active strategy by the cultural administration of the regional and local governments. In detail, this paper will analyse data relating to the development experienced, their characterisation through urban indicators or the evolution and traceability of their protection. In this sense, the use of 3D GIS will not only allow the efficient recording and the graphical representation of a significant amount of data resulting from the quantitative and qualitative analysis carried out but also model them using the third dimension to facilitate a cross analysis among the cities under study. Definitely, the aim is to demonstrate the suitability use of this technology in this type of scientific research.