Preventing the introduction of diseases, especially foreign animal diseases (FADs), and diseases that could cause food‐borne illness is critically important. Science‐based rules and regulations established by the United States Department of Agriculture (USDA) govern activities that could present homeland security risks. This article presents an overview of animal agriculture production in the United States and how that influences farm‐level control of pathogens, preventing and controlling the introduction of FADs by understanding the structure of food‐producing industries and the farm‐level vulnerabilities, and finally, farm‐level control of contemporary critical pathogens. The beef, poultry, and pork‐producing industries are discussed. The beef industry with its extensive nature of production in cow–calf operations is the most vulnerable to agroterrorism. The poultry industry is arguably the industry most protected from an agroterrorist attack. But the poultry and swine industries are still vulnerable, because the structure of these industries and the intensive production practices used has resulted in large numbers of animals located in relatively small geographic areas. So if an FAD outbreak does occur, the potential economic impacts are still very high. Contemporary FADs discussed in detail are highly pathogenic avian influenza (HPAI) foot‐and‐mouth disease (FMD), and classical swine fever (CSF).