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During the past decade, the implementation of 3D visualization and Geographic Information System (GIS) in archaeological research has increased and is now well established. However, the combination of these two factors remains rather complicated when faced with archaeological data. Some of the characteristics of this discipline impose the development of applications that will be able to cope with all of the specificities of archaeological data. Our research aims to create an Archaeological Information System (AIS) that will gather all of the characteristics of an archaeological work. In order to develop such an AIS, our first step was to identify its purposes and consequently, the features that should be available to the users. As it is destined to help with archaeological research, it is therefore of the outmost importance that the particularities of such a study are also taken into account. Moreover, the AIS is intended to incorporate point clouds that serve as a base for the three-dimensional model. These 3D point clouds result from the use of photogrammetry and/or lasergrammetry and, at a later stage, will be inserted into a GIS similar structure. The archaeological data will then be linked to the relevant section of the 3D model. However, these various stages and during the development of the AIS itself, we will encounter a series of issues that require to be addressed in order to produce a working system. This paper aims to identify and define the AIS characteristics as well as the issues and obstacles that we are going to face so that this system becomes a functional tool for archaeological research.