Food safety related to the consumption of animal-derived protein encompasses a wide variety of production and processing procedures which begins with the farm and inputs to the animals on the farm (e.g. feed and water) and includes the environment in which animals are reared. Hazards may be physical, artificial or naturally-occurring chemicals, organisms which cannot reproduce outside a specified life-cycle (e.g., parasites such as tapeworm in pigs) or viruses. Other microbes reproduce in the gastrointestinal tract of food animals as well as on the surface of food and in the environment. Methods of risk assessment for physical and chemical hazards have been used for many years. However, with microbial pathogens which can survive and grow on meat, in soil, water or other media, risk assessment methods are at the early stages of development. Due to the broad habitat range, the role of microbial pathogens in the food safety of meat, poultry, fruit and vegetables is important. The use of antibiotics in livestock species may accelerate the development of antibiotic-resistant strains of microbial pathogens, potentially complicating treatment for both animals and humans. The authors discuss the food chain, risk analysis and hazard analysis and critical control points in relation to foodborne pathogens, and introduce general strategies for improving pathogen control on the farm.