Since the first introduction of the term GIS in archeology, the archaeological community has made great strides in integrating GIS technology into its daily practice and many have recognized the value of geographic databases, digital cartography and spatial analysis in the management representation and analysis of the archaeological information. Over the last twenty years, research conducted at RC Athena and more recently at the Archaeological GIS Laboratory (AeGIS Athena http://aegis.athenarc.gr/) has sought to employ geospatial technologies in the archaeology of Northern Greece and to shed new light on the enormous potential of their application in the archaeological research. The purpose of this paper is to show and discuss the different possibilities and contribution of GIS applications through the employment of certain case studies. Moving from intra site analysis and data handling (University excavation in Karabournaki), to macro scale analysis (the study of the relationship between environment and settlement in Aegean Thrace) and the integration of GIS data with UNITY 3D we want to highlight the role of GIS systems as heuristic devices that will help us think about our assumptions and formulate our archaeological questions.