Massive facilities that keep large numbers of livestock have overtaken small, independent farms as the primary source of meat, eggs, and dairy in the United States. These concentrated animal feeding operations (“CAFOs”) compare more to industrial manufacturing operations than to traditional farms, and emit huge quantities of air pollutants that are harmful to public health, sickening people and damaging the environment. The Environmental Protection Agency (“EPA”) possesses statutorily provided tools under the Clean Air Act that it uses to regulate other polluting industries. However, this article – after reviewing the rise of CAFOs, examining the threats they pose, and surveying current regulation – suggests that the EPA’s approach to CAFOs is grossly inadequate. The article argues that the agency, under the Clean Air Act, should regulate the emissions of hydrogen sulfide and ammonia, two pollutants for which factory farms are major sources. This approach is incomplete, however. Pollutant-based regulation is both overbroad in that it will regulate other sources of these pollutants and underbroad because CAFO air pollution includes more than just these pollutants. The EPA should therefore additionally or alternatively rely on a more thorough and flexible pollution source-specific tool, the New Source Performance Standards (“NSPS”). NSPS are analogous to the rigorous source-specific approach used to regulate CAFO water pollution under the Clean Water Act, and will provide a comprehensive antidote to the ills of modern, industrial animal agriculture.