Atmospheric emissions from wildfires in Portugal were estimated yearly over the period 1990–2008 using Landsat-based burnt area maps and land cover maps, national forest inventory data, biometric models, and literature review data. Emissions were calculated as the product of area burnt, biomass loading per unit area, combustion factor, and emission factor, using land cover specific values for all variables. Uncertainty associated with each input variable was quantified with a probability density function or a standard deviation value. Uncertainty and sensitivity analysis of estimates were performed with Monte Carlo and variance decomposition techniques. Area burnt varied almost 50-fold during the study period, from about 9000ha in 2008 to 440000ha in 2003. Emissions reach maximum and minimum in the same years, with carbon dioxide equivalent (CO2eq.) values of 159 and 5655Gg for 2008 and 2003, respectively. Emission factors, and the combustion factor for shrubs were identified as the variables with higher impact on model output variance. There is a very strong correlation between area burnt and emissions, allowing for good emissions estimates once area burnt is quantified. Pyrogenic emissions were compared against those from various economy sectors and found to represent 1% to 9% of the total.