Unreinforced masonry (URM) aggregate buildings represent a significant portion of Italianbuilt heritage, especially in historical centers. These structures derive from the progressive transformation of structural units during the time, for example, because of the addition of new structural portions to existing ones. Masonry aggregates are characterized by a large number of possible configurations, including different interstorey heights, number of stories, different planar shapes and various arrangements of the masonry and structural details. Moreover, the degree of connection between the structural units is a relevant element of uncertainty conditioning the response. This paper presents a numerical study investigating the behavior of a reference-building aggregate by examining two different boundary conditions: the rigid diaphragm and the flexible diaphragm. The adopted numerical model employs a homogenized masonry approach by means of layered 2D shell elements. The models are realized with the STKO software platform for OpenSees. Nonlinear static analyses are carried out for the different case-studies highlighting the influence of the aforementioned parameters on the inplane response of the structural units and the extent of the so-called "aggregate effect".