The use of natural and organic fertilizers is increasing, as it makes it possible to use a significant amount of products from the rendering sector and the environment of livestock farming. This translates into the possibility of maintaining the appropriate biological, physical and chemical properties of the soil, and thus directly affects the state of the natural environment, as well as the safety of production of plant origin food (e.g. cereals, vegetables, fruit) and animal origin food, through feed. The threats from the above-mentioned sources should be properly identified, monitored and, after exceeding the critical values due to the achieved risk level, minimized. Many risk factors in this area are already identified and the relevant requirements are laid down in national and European Community law (e.g. on heavy metals, pathogens). An increasing issue is having comprehensive risk assessments of the potential presence of antimicrobial substances and microbial contamination in animal by-products, organic fertilizers, soil improvers and natural fertilizers. Pilot studies in this field were undertaken at the Department of Hygiene of Animal Feedingstuffs of the National Veterinary Research Institute in Puławy.