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Information on greenhouse gas (GHG) emissions from manure application in cropping systems of the irrigated mountain west region is needed. The objectives of this study were to (i) determine the effect of manure application rate and frequency (annual vs. biennial) on GHG losses compared to synthetic fertilizer, (ii) determine the effect of irrigation on GHG losses and (iii) determine the overall global warming potential (GWP) of using manure vs. synthetic fertilizer. Treatments included dry manure rates of 18 or 52 Mg ha(-1) applied annually or 36 Mg ha(-1) applied biennially as well as synthetic fertilizer and control treatments. Cumulative losses of N2O-N over the rotation ranged from 1.4 to 8.4 kg ha(-1) with the 52 Mg ha(-1) manure application losing the greatest amount of N2O-N. Emission factors for the growing season indicated that 0.13 to 0.24% of total N applied was lost as N2O-N. Cumulative CO2-C losses were greatest in the manure treatments, with approximately 7% of carbon added lost as CO2-C. Maximum N2O-N fluxes occurred at soil moisture contents of 0.3 to 0.4 m(3) m(3) and temperature near 25 degrees C, while CO2-C emissions occurred over broader soil moisture and temperature conditions. The overall GWP associated with manure application indicated a net negative GWP for manure treatments while the synthetic fertilizer treatment was near neutral. Including manure in cropping system rotations can lead to enhanced GHG emission, however the benefits of enhanced SOC can outweigh these losses leading to lower GWP than use of synthetic fertilizer alone.