Life cycle inventory models of greenhouse gas emissions from biofuel production have become tightly integrated into government mandates and other policies to encourage biofuel production. Current models do not include life cycle impacts of biomass storage or reflect current literature on emissions from soil and biomass decomposition. In this study, the GREET model framework was used to determine net greenhouse gas emissions during ethanol production from corn and switchgrass via three biomass storage systems: wet ensiling of whole corn, and indoor and outdoor dry bale storage of corn stover and switchgrass. Dry matter losses during storage were estimated from the literature and used to modify GREET inventory analysis. Results showed that biomass stability is a key parameter affecting fuel production per farmed hectare and life cycle greenhouse gas emissions. Corn silage may generate 5358 L/ha of ethanol at 26.5 g CO2 eq/MJ, relative to 5654 L/ha at 52.3 g CO2 eq/MJ from combined corn stover and conventional grain corn ethanol production, or 3919 L/ha at 21.3 g CO2 eq/MJ from switchgrass. Dry matter losses can increase net emissions by 3-25% (ensiling), 5-53% (bales outdoors), or 1-12% (bales indoors), decreasing the net GHG reduction of ethanol over gasoline by up to 10.9%. Greater understanding of biomass storage losses and greenhouse gas fluxes during storage is necessary to accurately assess biomass storage options to ensure that the design of biomass supply logistics systems meet GHG reduction mandates for biofuel production. (C) 2012 Elsevier Ltd. All rights reserved.