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In January of 2005, the United States Environmental Protection Agency (EPA) released the notice of the Animal Feeding Operations Consent Agreement and Final Order, offering animal feeding operations (AFOs) the opportunity to participate and help fund a nationwide emissions monitoring study that will be used to develop methodologies for estimating emissions from AFOs. As part of the Consent Agreement, ammonia and particulate matter emissions will be measured from swine, poultry, and dairy operations. This paper addresses the proposed protocol for measuring ammonia and particulate matter emissions as part of the EPA Consent Agreement.