Technical Abstract: Utilizing crop residues as biofuel feedstocks will involve trade-offs between bioenergy production and agroecosystem services. Consequently, agricultural production managers and policymakers need to critically evaluate current functions of crop residues in light of increasing demands for agricultural intensification including bioenergy. At issue are the short- and long-term impacts of residue harvest on the sustainability of soil resources and related food and energy production and the often disparate economic, environmental, edaphic, climatic, technological, and logistical factors involved. Although field studies cannot address all scenarios, long-term studies can provide insights on how crop residue harvest will impact key factors of agricultural sustainability such as soil organic matter (SOM). This topic was the major theme of the 2009 International American Society of Agronomy symposium entitled “Residue Removal and Soil Quality – Findings from Long-term Research Plots”. The papers in this special Agronomy Journal section were developed from this symposium and draw upon long-term studies from Europe, Canada, Australia and the USA to examine residue harvest impacts on SOM and factors related to long-term sustainably. In combination, these papers conclude that residue harvest will impact SOM, although the nature of the effects is situation-dependent. Also clear is that the assessment of harvesting residues must be placed in a farming systems context that includes an evaluation of economic and environmental trade-offs specific for a given farm and location. Therefore, future challenges include the development of science-based, site-specific decision aids that enable growers to make economically sound and environmentally sustainable choices.