Spatial variations of hazards such as strong ground motion and tsunami inundation are a key element for obtaining a geographical understanding of natural disasters. However, detailed distribution of tsunami run-up heights for the devastating tsunami associated with the 2011 off the Pacific coast of Tohoku earthquake is not available. A GIS analysis of tsunami inundation areas is conducted from data collected by the Tsunami Damage Mapping Team and from post-tsunami 2-m mesh and 5-m mesh digital elevation models (DEM) after the Geospatial Information Authority of Japan, in order to produce the Tsunami Run-up Height Map, which includes polygon data of inundation areas with elevation data at each point. Horizontal shifts of orthophotos taken just after the tsunami are corrected using a Helmert transformation. The map covers Iwate Prefecture, Miyagi Prefecture, and the northern part of Fukushima Prefecture continuously at high resolutions, and reveals spatial variations of tsunami run-up heights in detail. These variations are caused by: 1) landforms at each site, such as coastal plains, valleys, bays, and beach ridges, as well as their directions and magnitudes, and 2) source locations, interference, and wavelengths of the tsunami, as implied by a previous study. The map supports examination carried out on source fault models and simulation results of tsunamis from a geographical viewpoint. At the same time, the methodology to produce the map would be useful for systematically revealing run-up height distribution, in addition to inundation areas immediately after future tsunamis.