FDA
The FDA is an agency consisting of a number of centers and offices dealing with specific topics. It is part of the U.S. Department of Health and Human Services. The FDA is responsible for protecting the public health by assuring the safety and efficacy of drugs, biological products, medical devices, cosmetics, products that emit radiation and the nation's food supply. It is also responsible for advancing public health by making these products safer and more affordable, and ensuring information related to their use is publically available.
USDA
The USDA is a full federal government department headed by a cabinet member, the Secretary of Agriculture. It has a number of specific missions carried out by agencies under its supervision. These missions include assisting the country's farmers and ranchers from an economic and marketing perspective, food safety and work towards ending hunger. The USDA also is involved in protecting America's natural resources and environment as well as assisting rural communities through financial programs and loans.
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Different agendas
The FDA is involved in regulating drugs, medical products and potential health risks that are not in scope for the USDA. This can at times cause friction between the two agencies and their policies toward certain groups or businesses. One prime example would be tobacco products. While the FDA wants stronger regulation and would support the elimination of tobacco products, this would hurt the nation's tobacco farmers. Their protection and economic viability is a concern of the USDA, which can potentially be offering help and guidance to a group manufacturing a product that the FDA warns consumers to avoid.