The current increased focus on using forest residues and non-merchantable material for biofuels is generating an interest in understanding ecosystem effects of energy-wood harvesting. Scientists from the USDA Forest Service, University of Minnesota, and the U.S. Geological Survey reviewed 175 whole-tree harvesting studies and contrasted ecosystem effects of whole-tree harvesting, less-intensive conventional harvesting, natural disturbances, and energy-wood harvesting. They found a gradient of increasing departure from the structural conditions found after natural disturbance, when comparing conventional harvesting to whole-tree harvesting to energy-wood harvesting. Moreover, many functional aspects of forests, such as carbon storage, nutrient retention, species diversity, and interactions with aquatic ecosystems, increasingly depart from conditions found after natural disturbance along this same harvesting gradient. Although studying whole-tree harvesting provides good insight into the potential impacts of energy-wood harvesting, even these studies are limited when the latter includes removal of stumps, deadwood, and very small-diameter living stems. This level of removal and its effects on ecosystem function will need further study.