In the historical centres of Italy, masonry buildings are often found in aggregate configuration, in which geometrical complexity and structural heterogeneity coexist. In this paper, the influence of the masonry type -when combined with different floor types- on the seismic fragility of three aggregates prototypes is investigated through a numerical approach. The prototypes are representative of the historical residential building stock of Atella, a small town in the Basilicata region of Italy, and they consist of building aggregates differing in geometrical layout, but having similar age of construction, number of storeys, inter-storey height and wall thicknesses. Firstly, 24 structural models are developed through the 3Muri software for each building aggregate, by varying features of its vertical, horizontal and roof structures. Subsequently, non-linear static seismic analyses are performed on each model to obtain capacity curves. Based on the achieved results, mean typological fragility curves in terms of spectral displacement are obtained for each building aggregate, emphasising the role of the different masonry types identified on-site. Finally, a comparison between the three aggregate layouts is carried out to provide a seismic vulnerability assessment of the investigated historical centre.