Environmental regulations have historically been focused on individual emission points, facilities, or industrial sectors. However, recent and emerging regulations for greenhouse gas (GHG) emissions such as those contained in the Energy Independence and Security Act (EISA) of 2007 have introduced the concept of product life cycle limits on the emissions of transportation fuels. Thus, a complete life cycle assessment (LCA) of the transportation fuel must be completed where all emissions from field to the vehicle’s fuel tank and from tank to the vehicle’s exhaust must be assessed. However, although there have been extensive analysis of the GHG emissions associated with transportation fuels, there are substantial uncertainties associated with these estimates that can be attributed to poor data quality, inconsistent methodological choices, and model uncertainties, among others. This thesis evaluates the uncertainties present in LCA through the case study of fuel production using Fischer-Tropsch (F-T) synthesis of fuels derived from coal and biomass. Specifically, GHG emission estimates for F-T synthesis process scenarios are presented and the uncertainties in the estimates are discussed. Overall uncertainties in GHG emissions due to changes in the details of the process configurations in the F-T process can be up to 11%. This finding suggests that the details of fuel refining conditions will need to be specified in determining whether fuels meet GHG emission requirements, complicating the implementation of life cycle GHG regulations. / text