CO2 emission is a current global concern and has progressively increased due fossil fuel use, leading to climatic changes. As a workaround to this problem low carbon fuel use has been the key to mitigate it in several countries. Brazil is a leader in ethanol sugarcane production and has a high demand expected for this biofuel, which means that large areas will be cultivated to supply this demand. Although biofuels help to reduce carbon emissions, agriculture is highlighted in the emission of CO2 to the atmosphere as from the soil. Considering that the amount of soil carbon lost to the atmosphere is tightly coupled to the vegetation type, soil properties and climate conditions, the main objective of this study was to estimate and compare the CO2 emission in the agricultural phase of ethanol production, as from its main feedstocks. A model based on carbon flux of the soil-plant-atmosphere system, was used. From the five crops assessed (sugarcane, sugar-beet, corn, rice and cassava), sugarcane and corn crops presented, the less CO2 emission at nowadays and over the next 30years, in opposite of the sugar-beet crop, which was the less sustainable feedstock for ethanol production in terms of CO2 emission. The outcomes of this study contribute to develop scenarios to better understand the impact of ethanol production in the GEEs emission, both in nowadays and in the future, considering the increasing demand for biofuel. Also is presented in this study a detailed discussion regarding important environmental issues of sugarcane and corn ethanol production, which are essential to be considered in the ethanol-policy decision. To our knowledge this is the first study that compares the CO2 emitted from the main ethanol feedstocks based on field tests, under the same conditions of soil and climate.