Ammonia (NH(3)) emissions from animal systems have become a primary concern for all of livestock production. The purpose of this research was to establish the relationship of nitrogen (N) emissions to specific components of swine production systems and to determine accurate NH(3) emission factors appropriate for the regional climate, geography, and production systems. Micrometeorological instrumentation and gas sensors were placed over two lagoons in North Carolina during 1997-1999 to obtain information for determining ammonia emissions over extended periods and without interfering with the surrounding climate. Ammonia emissions varied diurnally and seasonally and were related to lagoon ammonium concentration, acidity, temperature, and wind turbulence. Conversion of significant quantities of ammonium NH(4)(+) to dinitrogen gas (N(2)) were measured in all lagoons with the emission rate largely dependent on NH(4)(+) concentration. Lagoon NH(4)(+) conversion to N(2) accounted for the largest loss component of the N entering the farm (43% as N(2)); however, small amounts of N(2)O were emitted from the lagoon (0.1%) and from field applications (0.05%) when effluent was applied nearby. In disagreement with previous and current estimates of NH(3) emissions from confined animal feeding operation (CAFO) systems, and invalidating current assumptions that most or all emissions are in the form of NH(3), we found much smaller NH(3) emissions from animal housing (7%), lagoons (8%), and fields (2%) using independent measurements of N transformation and transport. Nitrogen input and output in the production system were evaluated, and 95% of input N was accounted for as output N from the system.