Here we present an uncertainty analysis of NH3 emissions from agricultural production systems based on a global NH3 emission inventory with a 5×5 min resolution. Of all results the mean is given with a range (10% and 90% percentile). The uncertainty range for the global NH3 emission from agricultural systems is 27–38 (with a mean of 32) Tg NH3-N yr−1, N fertilizer use contributing 10–12 (11) Tg yr−1 and livestock production 16–27 (21) Tg yr−1. Most of the emissions from livestock production come from animal houses and storage systems (31–55%); smaller contributions come from the spreading of animal manure (23–38%) and grazing animals (17–37%). This uncertainty analysis allows for identifying and improving those input parameters with a major influence on the results. The most important determinants of the uncertainty related to the global agricultural NH3 emission comprise four parameters (N excretion rates, NH3 emission rates for manure in animal houses and storage, the fraction of the time that ruminants graze and the fraction of non-agricultural use of manure) specific to mixed and landless systems, and total animal stocks. Nitrogen excretion rates and NH3 emission rates from animal houses and storage systems are shown consistently to be the most important parameters in most parts of the world. Input parameters for pastoral systems are less relevant. However, there are clear differences between world regions and individual countries, reflecting the differences in livestock production systems.