Biomass energy is the oldest form of energy harnessed by humans. Currently, processed biofuels, which are derived from biomass, are being pursued as a possi- ble route to decarbonize the transport sector—a particularly difficult task for both technological and sociological reasons. In this thesis I explore the impacts that large scale biofuel use could have on atmospheric chemistry. I review the current state of biofuels politically and technologically, focusing on ethanol and biodiesel. I discuss the salient features of tropospheric chemistry and in particular the oxidation of isoprene, an important biogenic volatile organic compound. I examine the impact that including isoprene oxidation has in a new chemistry-climate computer model, UKCA; the response of ozone turns out to depend on local chemical conditions. To evaluate the global model, I use data from the OP3 field campaign in Malaysia and compare it with output from the model chemical mechanism. The mechanism is able to reproduce NOx and ozone measurements well, though is more sensitive to representations of physical rather than chemical processes. I also perform a simple sensitivity study which examines crop changes in the region of Southeast Asia. In the final two chapters, I turn to two distinct phases of the biofuel life cycle. I characterize a potential future atmosphere through an ozone attribution study, then examine the impact of future cropland expansion (phase I of a biofuel life cycle) on tropospheric chemistry. I find that land use change has a large impact on ozone, and that it is more acute than another perturbation (CO2 suppression) to isoprene emissions. I then move to phase III of the life cycle—combustion—and look at the sensitivity of the model chemistry to surface transport emissions from biofuels as a replacement for conventional fuels. I find that biodiesel reduces surface ozone, while ethanol increases it, and that the response has both a linear and nonlinear component.