Wilderness designation continues to be a contentious effort and must be fully justified even in wealthy countries such as the USA. An important consideration in setting priorities for additional designations of Wilderness is to ensure that under-represented ecosystems are protected. The utility of Geographic Information Systems in performing this task is illustrated using data on ecoregions and areas in the National Wilderness Preservation System to determine the relative protection currently afforded to different ecoregions in the continental USA. We find that 23 of the 35 ecoregions have less than 1% of their land area protected as Wilderness, and 7 of the 35 have no land protected as Wilderness whatsoever. While much of the land with little protection is in areas dominated by private land ownership in the mid-west and southeast, a surprisingly large amount of land in the Intermountain states of Nevada and Utah, which is in public ownership, is substantially under-represented in the National Wilderness Preservation System as well. The implications of this analysis for wilderness allocation strategies are detailed. The technique illustrated in this paper is a useful aid in designing protected area strategies in countries throughout the world.