Pesticide, fertilizer, and herbicide programs must be monitored to ensure that they do not interfere with food production. For example, growing and harvesting periods should be noted to reduce the risk of residues in the food products.

Water quality affects all agricultural commodities.
Using potable water is recommended for feeding animals and crops.
During crop production potable water should be used for irrigation, as well as for the application of pesticides, herbicides, and fertilizers.

Ground beef is considered adulterated if it is contaminated with the specific type of bacteria called Escherichia coli O157:H7. This type of bacteria produces toxins and is different from the generic E. coli which lives in the human intestine.

Fruits and vegetables should be produced and harvested following ‘Good Agricultural Practices’ (GAPs).
This program contains specific guidelines for managing the following broad issues: water, manure and municipal biosolids, worker health and hygiene, sanitary facilities, field sanitation, packing facility sanitation, and transportation.
The number of foodborne outbreaks associated with fruits and vegetables has increased significantly over the past ten years.

Dairy: Animal health and well-being is an important concern for reducing any pre-harvest food safety risks. Traditionally the process of pasteurization can be relied upon to inactivate potential pathogens that can be transmitted in raw milk. With the emergence of the "raw diet" and an increase the numbers of persons who wish to consume unpasteurized milk we have seen an increase in foodborne illness associated with the consumption of this product. It is important to know if your milk is pasteurized before drinking it and if you choose to consume unpasteurized milk you should be aware of the risks.

Sheep and goats may be rasied for milk and/or meat production. The ways in which the animals are raised is important in the safety and quality of the final food products. It is essential that the animals are of good genetic stock, are treated humanely while being raised, and maintain good health.

The food safety of pork products begins with good animal health and herd management to reduce the risk of bacterial, viral, and parasite contamination.

Animal feed must be stored under specified conditions to reduce mold and subsequent aflatoxin production.
Ruminant feed bans have been in place since 1997 to reduce the risk of Bovine Spongiform Encephalopathy (BSE, commonly know as Mad Cow disease) in the United States.

Salmonella and Campylobacter are natural flora of avian species and while they do not cause disease in birds, they can lead to illness in humans from the consumption of undercooked meat or in the case of cross-contamination.

Organic agriculture includes fresh produce and animals that have been raised organically following standards instituted by the United States Department of Agriculture (USDA) National Organic Program (NOP). This program certifies products are organically grown and rasied including restricting the use of synthetic pesticides, genetically modified ingredients and feeds, and irradiation. Organically raised foods are not necessarily more healthy or safe than conventionally raised foods.

Eggs are an excellent source of protein for humans. In shell eggs are regulated by the US Food and Drug Administartion while out of shell egg products are regulated by the US Department of Agriculture (USDA). Both regulatory bodies work to maintain the safety and quality of the eggs. On the farm programs include reducing the presence of Salmonella Enteritidis which may be transmitted through undercook eggs. It is important to store, handle, and cook eggs properly to avoid foodborne illness.

Seafood include fin fish and shellfish that may be raised in a variety of ways. Of course the water that these animals come into contact with is important. Shellfish are filter feeders and may filter out viruses if they are present in the water which can cause illness if consumed raw. Fin fish are extremely heathy and a great source of omega-3-fatty acids and other nutrients. While there are risks associated with teh consumption of fish the benefits outweigh these risks.