Ever since the Kyoto Protocol, agroforestry has gained increased attention as a strategy to sequester carbon (C) and mitigate global climate change. Agroforestry has been recognized as having the greatest potential for C sequestration of all the land uses analyzed in the Land-Use, Land-Use Change and Forestry report of the IPCC; however, our understanding of C sequestration in specific agroforestry practices from around the world is rudimentary at best. Similarly, while agroforestry is well recognized as a land use practice capable of producing biomass for biopower and biofuels, very little information is available on this topic. This thematic issue is an attempt to bring together a collection of articles on C sequestration and biomass for energy, two topics that are inextricably interlinked and of great importance to the agroforestry community the world over. These papers not only address the aboveground C sequestration, but also the belowground C and the role of decomposition and nutrient cycling in determining the size of soil C pool using specific case studies. In addition to providing allometric methods for quantifying biomass production, the biological and economic realities of producing biomass in agroforestry practices are also discussed.