Biological agents, bacteria, viruses and parasites can, directly or indirectly, contaminate food. Similarly chemicals such as veterinary drugs used to combat animal illnesses, mycotoxins particularly aflatoxins, pesticides and environmental contaminants (e.g. dioxins, heavy metals) in animal feeds can also be a source contamination of food. Contamination of agricultural, animal and fish products is the result of the presence of human pathogenic bacteria and/or toxic substances, which can contaminate products in any part of the production chain. Examples are of the presence of a wide range of pathogens such as Salmonella spp., pathogenic Escherichia coli and Shigella, hepatitis A virus on fresh fruits and vegetables, E. coli O157:H7 in meats, Campylobacter spp., Brucella spp. in milk, Vibrio sp. and ciguatera toxin in fish. Thus the importance of good practices at the primary production level to prevent diseases and infections in animals, minimize risk of transmission to humans and/or contamination of food as well as to ensure animal health and welfare. The authors address three main primary production systems and the challenges to reduce the safety threats inherent to each. Good animal farming, fish health and good agricultural practices are described extensively so as to provide a clear picture of the complexity of the food production chains and the many factors that need to be under control to ensure the safety of food products.