Approximately 80 different crop species are grown in the United States in widely differing geographic areas, climatic and edaphic conditions, and management practices. Although the majority of cultivated acreage in the United States is planted with only about 10 primary crops, uncertainties associated with trace gas emissions arise from: (1) limited data availability, (2) inaccurate estimates because of large temporal and spatial variability in trace gas composition and magnitude of trace gas emissions from agricultural activities, (3) differing characteristics of pollutant emissions from highly dispersed animal feed-lots, and (4) limited understanding of the emissions of semi-volatile organic compounds (SVOCs) associated with agriculture. Although emission issues are of concern, so also is atmospheric deposition to cropping systems, including wet and dry nitrogen, minerals, and organic compounds. These can have feedback effects on trace gas emissions. Overall, the many gaps in our understanding of these aspects of agricultural systems deserve serious attention.