What’s the Difference Between the FDA and the USDA?

Explaining America’s weirdly complicated food inspection system, including who regulates poultry and eggs and how Robert F. Kennedy Jr. is involved

Almost everything Americans eat — including the food on restaurant menus across the country — has been vetted by one of two government agencies: the Food and Drug Administration (FDA) or the United States Department of Agriculture (USDA). The Center for Food Safety and Applied Nutrition (CFSAN), which is a part of the FDA, regulates drugs and dietary supplements, and ensures, according to government language, that the foods people eat in the U.S. “are safe, wholesome, sanitary and properly labeled.” The USDA, meanwhile, works to support the American agricultural economy and “provide a safe, sufficient, and nutritious food supply for the American people.”

On February 13, Robert F. Kennedy Jr. was confirmed to lead the Department of Health and Human Services, which oversees the FDA. Kennedy holds a number of controversial food policy positions, including advocating for the consumption of raw milk. Martin Makary, a former surgeon at Johns Hopkins and critic of vaccine mandates, will lead the FDA under Kennedy. Brooke Rollins, a policy aide who worked in the first Trump administration, is now Secretary of Agriculture, meaning that she will lead the USDA, which is totally separate from the Department of Health and Human Services.

Needless to say, there are several confusing divisions between the two agencies. The USDA mainly oversees meat, poultry, and eggs — but under its umbrella also falls the Center for Nutrition Policy and Promotion, which establishes Dietary Guidelines, and the Food and Nutrition Service, which administers SNAP benefits (aka food stamps). The FDA, meanwhile, is responsible for regulating — and slapping a nutrition facts label — on all processed foods created and sold in the U.S.

The humble pepperoni pizza exemplifies the complicated way in which these two agencies interact — or don’t. Usually, the only difference between a cheese pizza and a pepperoni pizza is the pepperoni. Yet a frozen pepperoni pizza, because it contains meat, will go through three separate USDA inspections: At the slaughterhouse, at the pepperoni-making facility, and at the pizza factory. Meanwhile, a frozen cheese pizza usually only needs approval from the FDA once: when the pizza manufacturer adds a nutritional label.

Though many Americans may think the USDA is the main inspection arm of the U.S. government — due to its more visible logo on meats and organic certifications — it’s actually the FDA that regulates about 78 percent of the U.S. food supply, including dairy, seafood, produce, packaged foods, bottled water, and eggs. (The USDA’s meat grades come out of its marketing branch, which is part of the reason why those blue stamps feature the USDA logo so prominently. The FDA’s logo doesn’t appear on the millions of nutrition labels it approves each year.)

The FDA does not itself inspect restaurants, but in addition to green-lighting the packaged food available for purchase in America, its Food Code is what city and state Departments of Health use when inspecting local businesses. The Code is meant to keep food at safe temperatures and conditions so as to prevent foodborne illness and the spread of disease.

During the first Trump administration, his appointees loosened inspection requirements at pork plants and chicken egg production facilities, which caused alarm among food safety experts. His presidency had significant impacts on agriculture, farm labor, and school lunch programs, and it’s likely that this second term will be equally impactful, which is why it’s important to know who’s handling which parts of the American food chain. Here’s a brief breakdown of the two agencies’ purviews.

How does the government regulate meat?

The USDA’s internal Food Safety and Inspection Service regulates almost all of the meat we eat, including beef, pork, goat, and lamb (and poultry, see below). Safety inspections are mandatory, but the USDA’s Agricultural Marketing Service also offers producers the option to grade meat. This extra service, which comes with a fee, is why consumers will see meat cuts labeled “USDA Prime” or “USDA Choice” at the grocery store. Diners will note these distinctions, used to indicate quality, on many steakhouse menus.

The FDA, meanwhile, regulates “meat from exotic animals,” which includes venison and other hunted game like wild boar. The USDA is responsible for inspecting sausages, but the FDA inspects sausage casings (because, as FoodSafetyNews writes, “they have no nutritional value as meat.”)

Which organization inspects poultry?

The USDA inspects domesticated chicken, turkey, duck, and goose, as well as canned chicken products. This agency also has established processes for handling the avian influenza epidemic, which range from mandatory testing of poultry products to slaughtering birds to prevent the spread of the virus.

Is the USDA or FDA responsible for keeping our egg supply safe?

Representatives from the USDA and FDA acknowledge that laws surrounding the regulation of eggs are murky and vary from product to product. In general, the USDA inspects egg products, like packaged egg whites and powdered eggs used in food processing, while the FDA regulates whole eggs in their shells. (Again, USDA-graded eggs are a part of the branch’s marketing arm, and do not reflect inspection for safety.) Egg substitutes and replacements (which do not contain any egg product) are regulated by the FDA.

Which organization handles dairy regulation?

The FDA regulates packaged milk and dairy in the U.S., including yogurt, sour cream, cheese, and ice cream that does not contain eggs. The FDA has specific rules for different kinds of cheeses, including how much moisture and milk fat they must contain, and what aging times are required for cheeses made from raw, or unpasteurized, milk.

In light of the 2025 avian influenza, also known as H5N1 or “bird flu,” outbreaks across the country, the agency has also established the National Milk Testing Strategy, which will “facilitate comprehensive H5N1 surveillance of the Nation’s milk supply and dairy herds” in an effort to better understand how to combat the virus. The agency is also researching a vaccine for the virus that could be given to dairy cows to prevent the spread of H5N1.

Who’s in charge of regulating fish?

The FDA regulates fish, shellfish, and all seafood — except farmed catfish, the production of which is inspected by the USDA. When foods are recalled by their suppliers in the event of contamination, like the recent recall of major canned fish brands possibly contaminated with botulism, the FDA publicizes those recalls to help ensure that people who have purchased recalled products can return or dispose of them before consuming them.

Which organization tackles produce?

Raw fruits and vegetables fall under the regulation of the USDA, but once they’re processed — into applesauce or bottled juice or dried fruit chips — they become the FDA’s problem.

So then does the FDA handle packaged foods?

Yes. The production of packaged foods like Cheez-Its, Starburst, Lucky Charms, grab-and-go salads, frozen pizza, and jars of peanut butter and jelly are all subject to FDA inspection and regulation.

However, when meat shows up on packaged sandwiches and pizza interesting exceptions to USDA/FDA rules emerge. Open-faced meat sandwiches, where the ratio of meat to bread and other ingredients is more than half, are regulated by the USDA. But closed sandwiches, which have two slices of bread, are regulated by the FDA because the ratio of meat to other ingredients is less than 50 percent.