Using a revised Intergovernmental Panel on Climate Change (IPCC) methodology and the process-based model DeNitrification and DeComposition (DNDC), we estimated N2O emissions from agroecosysterns in Canada for each census year from 1981 to 2001. Based on the IPCC methodology, direct emissions of N2O ranged from 12.9 to 17.3 with an average of 15.1 Tg CO2 equivalents, while the DNDC model predicted values from 16.0 to 24.3 with an average of 20.8 Tg CO2 equivalents over the same period, and showed a large interannual variation reflecting weather variability. On a provincial basis, emissions estimated by IPCC and DNDC methods were highest in Alberta, Saskatchewan and Ontario, intermediate for Manitoba and Quebec and lowest in British Columbia and the Atlantic provinces. The greatest source of emissions estimated by the IPCC method was from N fertilizer (avg. 6.32 Tg CO2 equiv. in Canada), followed by crop residues (4.24), pasture range and paddocks (PRP) (2.77), and manure (1.65). All sources of emissions, but especially those from fertilizers, increased moderately over time. Monte Carlo Simulation was used to determine the uncertainty associated with the 2001 emission estimates for both IPCC and DNDC methodologies. The simulation generated most likely values of 19.2 and 16.0 Tg CO2 equivalents for IPCC and DNDC, respectively, with uncertainties of 37 and 41%, respectively. Values for the IPCC estimates varied between 28% for PRP and manure and 50% for N fertilizer and crop residues. At the provincial level, uncertainty ranged between 15 and 47% with higher values on the prairies. Sensitivity analyses for IPCC estimates showed crop residues as the most important source of uncertainty followed by synthetic N-fertilizers. Our analysis demonstrated that N2O emissions can be effectively estimated by both the DNDC and IPCC methods and that their uncertainties can be effectively estimated by Monte Carlo Simulation.