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Agricultural soils are important sources of atmospheric N2O and CO2. However, in boreal agro-ecosystems the contribution of the winter season to annual emissions of these gases has rarely been determined. In this study, soil N2O and CO2 fluxes were measured for 6 years in a corn-soybean-wheat rotation in northeast China to quantify the contribution of wintertime N2O and CO2 fluxes to annual emissions. The treatments were chemical fertilizer (NPK), chemical fertilizer plus composted pig manure (NPKOM), and control (Cont.). Mean soil N2O fluxes among all three treatments in the winter (November–March), when soil temperatures are below −7°C for extended periods, were 0.89–3.01 µg N m−2h−1, and in between the growing season and winter (October and April), when freeze-thaw events occur, 1.73–5.48 µg N m−2h−1. The cumulative N2O emissions were on average 0.27–1.39, 0.03–0.08 and 0.03–0.11 kg N2O–N ha−1 during the growing season, October and April, and winter, respectively. The average contributions of winter N2O efflux to annual emissions were 6.3–12.1%. In all three seasons, the highest N2O emissions occurred in NPKOM, while NPK and Cont. emissions were similar. Cumulative CO2 emissions were 2.73–4.94, 0.13–0.20 and 0.07–0.11 Mg CO2-C ha−1 during growing season, October and April, and winter, respectively. The contribution of winter CO2 to total annual emissions was 2.0–2.4%. Our results indicate that in boreal agricultural systems in northeast China, CO2 and N2O emissions continue throughout the winter. [ABSTRACT FROM AUTHOR]