A hundred years have passed since the publication of the first volume of the Geschiedkundige Atlas van Nederland [Historical Atlas of the Netherlands] under supervision of Anton Beekman et al. In total, it encompassed 30 descriptive volumes and countless maps of the Netherlands and its colonies, from the Roman times to the nineteenth century. With the advent of the computer, techniques to create and analyse maps have developed rapidly, and increasingly are attracting the interest of humanities scholars as well. In contrast to printed maps, digital GIS maps allow the user to easily combine different maps or information layers and analyse these more thoroughly. Though this has led to many interesting spatial humanities projects, for the Netherlands most notably the HISGIS.nl project which aims at creating a national atlas of buildings and plots of land using early cadastre maps, the maps by Beekman et al. are yet to be surpassed as the principal source for historical boundaries in the Netherlands. This digital GIS dataset contains historical boundaries of cities, parishes, heerlijkheden, and other meaningful entities in the Medieval and Early Modern Low Countries. Its creation involves the selection of sources, including historical maps, the drawing of digital maps, and the creation of a data model for the maps and related historical statistics. As the project is expanding, issues such as data curation and data access need attention as well. The principal reason for creating these maps is the desire to be able to tie socioeconomic developments to specific geographic contexts. The map creates the conditions to geographically define historical statistics much more precise than before. Current emphasis in the project lies on linking the maps to all available Late Medieval surveys stating the number of hearths in the various parts of the Low Countries. These surveys have also turned out to be a crucial element in the methodology for the creation of the GIS maps. Currently, the dataset covers the Duchy of Brabant, the County of Holland (including a careful reconstruction of pre-flood boundaries of 1421), the County of Zeeland (prior to the 1530/32 floods), the County of Hainaut, the County of Artois, the Prince-Bishopric of Liège, the Prince-Bishopric of Thérouanne, the Prince-Bishopric of Cambrai, the Lordship of Mechelen, the Lordship of Vianen, and the Lordship of Ravenstein. Close to completion are the maps of Utrecht (including Overijssel), Guelders, Cleves (partially), Picardy (Amiens, Ponthieu, Vermandois, Eu), Boulonnais, Flanders, Tournaisis, Namur, Luxembourg, Stavelot-Malmédy, Limbourg, Bentheim, and various smaller areas. Work will start soon on Friesland, Groningen, Drenthe, Jülich. The current version of the dataset focuses on the period around 1500. The ultimate goal is a digital GIS map of historical boundaries, stretching from the north of France to the Waddenzee in four cross-sections (1350, 1500, 1650, and 1800), which can be used for various historical research. For users that are not necessarily interested in village-level GIS boundaries, but do need (shifting) boundaries of the territories in the Low Countries (Middle Ages - present), such a scholarly resource is available for public use here (please use customary citation standards). This geodataset can be seen live in action here.