The historical and architectural heritage preservation is a very important task for seismically vulnerable European countries. Medieval masonry towers and bell towers in churches are quite diffused all over Europe as an essential part of the cultural heritage to be preserved. In fact, recent earthquakes highlighted that ancient masonry towers are particularly susceptible to either partial or total collapse under seismic excitations but modelling their behaviour at various levels of accuracy is still an open field of research. In order to shed some light on the role played by aggregate buildings on the seismic response of historic towers, their safety assessment is investigated in the current paper starting from the case study of the Sciri tower in Perugia. Firstly, linear dynamic analysis by means of the SMuri software is conducted with the aim to identify the main vibration modes of the tower. To this purpose, the tower is modelled both as an isolate structure and in aggregate condition within the urban built-up. Subsequently, the numerical fundamental period of the tower is compared with results deriving from different literature empirical methods in order to find the most effective predictive relationship. Finally, the seismic behaviour difference between the isolate tower and the aggregate one is assessed in terms of vibration periods, focusing, in particular, on the variation of vibration frequencies associated to the variation of the tower free height from the ground.