Engineering infrastructure of modern cities represents a rather complex hierarchical system, which involves the structuring of the design process into separate subsystems taking into account the prospects of their development and reconstruction. While designing communications the technical and economic feasibility of their construction at the appropriate place should be considered, as it impacts the efficiency of future communication. In this regard, it is urgent to create specialized geographic information systems (GIS), allowing to estimate the projected cost of utilities prior to commencement of construction works, and to take into account the spatial location of the various utilities, their multi-level nature and interaction. The main aim of the study: development of creation concept of the specialized GIS based on model hyper networks, allowing the designer or user to consider the spatial location of the various utilities, their multi-level nature and interaction in the organization and management of engineering infrastructure of cities. The methods used in the study: grid method in the construction of terrain models in the form of a discrete analogue of the staging area; methods of graph theory to find the optimal routes for laying of engineering networks; methods of the theory of hyper networks to describe the multi-levelness of creation of engineering infrastructure of modern cities. The results. The authors introduced a hyper network technology of creation of the specialized geographic information systems, which is based on the hypernetwork models and structuring of the design process into separate subsystems. The proposed approach, unlike traditional methods of creation of GIS-technologies, allows organizing optimal spatial placement of engineering utilities for various purposes at the stage of their design taking into account their interrelation and interdependence. The conclusions: the proposed method of creation of the specialized GIS, which is based on the hypernetwork models, allows taking into account special features of the real terrain, the type and purpose of the designed communication.