Increasing the use of biofuels influences atmospheric greenhouse gas concentrations. Although widely recognized, uncertainties related to the particular impacts are typically ignored or only partly considered. In this paper, various sources of uncertainty related to the GHG emission savings of biofuels are considered comprehensively and transparently through scenario analysis and stochastic simulation. Technology and feedstock production chain-specific factors, market-mediated factors and climate policy time frame issues are reflected using as a case study Fischer-Tropsch diesel derived from boreal forest biomass in Finland. This case study shows that the GHG emission savings may be positive or negative in many of the cases studied, and are subject to significant uncertainties, which are mainly determined by market-mediated factors related to fossil diesel substitution. Regardless of the considerable uncertainties, some robust conclusions could be drawn; it was likely of achieving some sort of but unlikely of achieving significant savings in the GHG emissions within the 100 year time frame in many cases. Logging residues (branches) performed better than stumps and living stem wood in terms of the GHG emission savings, which could be increased mainly by blocking carbon leakage. Forest carbon stock changes also significantly contributed to the GHG emission savings.