Due to changes in carbon stock of soil and biomass, indirect land-use change (ILUC) has consequences on green house gas (GHG) balance of a biofuel that are not presently considered in evaluation of environmental merits of biofuels. Significant changes in land-use are expected to occur in biofuel producing countries and their consequences may affect global markets. This paper aims to: 1) Review state-of- art of accounting for indirect effects in biofuels production and their influence on GHG balance of a biofuel pathway; 2) Present a model to estimate and optimize GHG emissions from LUC; and 3) Estimate potential GHG emissions for the case of soybean-based biodiesel production. ILUC concepts and a classification of ILUC sources are proposed. Then a methodological framework to quantify GHG emissions is discussed and applied to the case study. Different scenarios to achieve demand are proposed and their implications related to ILUC are determined. Using a system-wide approach and a non-linear programming (NLP) model, GHG emissions are evaluated in terms of carbon pay back time and optimized based on soybean supply strategy to produce biodiesel.