A global biofuels program will potentially lead to intense pressures on land supply and cause widespread transformations in land use. These transformations can alter the Earth climate system by increasing greenhouse gas (GHG) emissions from land use changes and by changing the reflective and energy exchange characteristics of land ecosystems. Using an integrated assessment model that links an economic model with climate, terrestrial biogeochemistry, and biogeophysics models, we examined the biogeochemical and biogeophysical effects of possible land use changes from an expanded global second-generation bioenergy program on surface temperatures over the first half of the 21st century. Our integrated assessment model shows that land clearing, especially forest clearing, has two concurrent effects—increased GHG emissions, resulting in surface air warming; and large changes in the land's reflective and energy exchange characteristics, resulting in surface air warming in the tropics but cooling in temperate and polar regions. Overall, these biogeochemical and biogeophysical effects will only have a small impact on global mean surface temperature. However, the model projects regional patterns of enhanced surface air warming in the Amazon Basin and the eastern part of the Congo Basin. Therefore, global land use strategies that protect tropical forests could dramatically reduce air warming projected in these regions.