The US EPA and USDA recently commissioned the National Research Council to review the state of the science of emissions from animal feeding operations in the US. That study concluded that these agricultural activities are a major, or even dominant source of several pollutants including ammonia. It further concluded that it is not currently possible to quantify accurately emissions factors, or, as would be more appropriate, quantify emissions as a function of local meteorology, climate, geography and farming practices. Mass balance approaches to the N budget of animal feeding operations, however, provide substantial evidence for the loss of large quantities of ammonia from the system. In the troposphere, ammonia plays only a minor role in the NOx budget and smog chemistry, although it may be a source of N2O under some circumstances. In the condensed phase, however, ammonia is a major component of aerosols, and aerosols have major effects on human health, visibility, and climate. Ammonia can alter the microphysical properties of aerosols to increase the rate of new particle formation. Ammonium can make particles more hydroscopic and alters their properties as cloud condensation nuclei - changing climate through what is called the indirect effect. Haze from ammonia-containing aerosols not only limits visibility but alters the radiative balance of the atmosphere with implications for atmospheric stability, precipitation, photochemistry, and climate.