Estimating CO2 emission factor of the electricity system is a key aspect in the calculation of the baseline emissions for projects certified as Clean Development Mechanism (CDM), which replace energy from the grid. Uruguay is currently driving the expansion of the electricity system based on domestic renewable energies, in addition to replacing oil-based fuels for others with lower emission factors. This implies a substantial change of the generation park in the next decade and of the associated CO2 emissions. In this paper a calculation methodology of the baseline emissions is adapted for its incorporation in the software SimSEE (Electric Energy Systems Simulator), which is used for modeling the Uruguayan electric system, and therefore allows modeling the current energy generator park and the future one. Using this tool, the CO2 emission factor’s evolution is evaluated in the 2012-2020 period. The 2020 scenario is based on an optimal expansion of the electric system. The results indicate a strong reduction of the emission factor between 2012 and 2020, going from average values (for 100 simulations) around 0.60 tCO2 /MWh to 0.15 tCO2/MWh. In this possible future scenario, CDM certification will probably not act as a strong incentive in Uruguay for the development of projects based on non-traditional renewable energies.