We show in this study that a full fuel-cycle analysis of the greenhouse gas (GO,) implications of biomass energy systems has not only to take into account the inputs and outputs of energy (and associated carbon content) but must recognize that many biomass systems have by-products that are produced along with the biofuel. The analysis must also account for the temporal variability of carbon stocks and fluxes associated with the standing biomass and its harvest. Where land resources are limited, we need to consider the opportunity cost of managing the land to produce biomass fuels. Establishing a system of parties, each accountable for its own greenhouse-gas emissions, would require detailed deliberations on how to treat carbon flows in biofuels and wood products exchanged between the parties. An accounting for credits and debits has to be found that encourages each party to act in a way that is optimal for the carbon budget of the whole system.