Geographic Information Systems (GIS) are being applied with increasing frequency, and with increasing sophistication, in international relations and in political science more generally. Their benefits have been impressive: analyses that simply would not have been possible without GIS are now being completed, and the spatial component of international politics—long considered central but rarely incorporated analytically—has been given new emphasis. However, new methods face new challenges, and to apply GIS successfully, two specific issues need to be addressed: measurement validity and selection bias. Both relate to the challenge of conceptualizing nonspatial phenomena with the spatial tools of GIS. Significant measurement error can occur when the concepts that are coded as spatial variables are not, in fact, validly measured by the default data structure of GIS, and selection bias can arise when GIS systematically excludes certain types of units. Because these potential problems are hidden by the technical details of the method, GIS data sets and analyses can sometimes appear to overcome these challenges when, in fact, they fail to do so. Once these issues come to light, however, potential solutions become apparent—including some in existing applications in international relations and in other fields.