In 1998 the National Plant Genome Initiative (NPGI) was established as a coordinated national research program by the Interagency Working Group (IWG) on Plant Genomes with representatives from the U.S. Department of Agriculture (USDA), U.S. Department of Energy (DOE), National Institutes of Health (NIH), National Science Foundation (NSF), Office of Science and Technology Policy (OSTP), and Office of Management and Budget (OMB). The current IWG also includes the U.S. Agency for International Development (USAID). Since 1998, the field of plant genomics has been revolutionized by the freely accessible tools and resources developed through the NPGI. The NPGI has changed the way research is conducted in plant biology and beyond; it has attracted a new generation of scientists to plant research; and it has contributed new knowledge and ideas to science. Through the development of plant genomic and other "-omics" resources, the NPGI has built a foundation on which the scientific community is advancing research, not just in plant genomics but across diverse disciplines spanning the biological sciences. This report describes the NPGI plan for the next five years (2009 - 2013). The IWG based this plan on a wide range of inputs from the broader community which are listed in the Appendix.