Organic fertilizers are an essential source for plant nutrients and a soil conditioner in agriculture. Due to its sources and the composition of the organic inputs as well as the type, functionality and failures of the applied treatment process, the organic fertilizer may contain various amounts of infectious agents and toxic chemicals, especially the antibiotics that can be introduced to the subsequent food chain. A range of human and animal pathogens of bacterial, viral and parasitic origin have been the cause of foodborne epidemics due to unintended contamination from organic fertilizers. The use of antibiotics by humans and in animal feeds will also end up in the organic fertilizers. These antibiotics and other chemicals, depending on the sources of the organics, will enhance the likelihood of occurrence of resistant and multi-resistant strains of microorganisms in society and have been reported to cause ecotoxicological environ‐ mental effects and disruption of the ecological balance. Exposure of microorganisms to sublethal concentration of antibiotics in the organic products induces antibiotic resistance. WHO guidelines for the reuse of excreta and other organic matters identify the risk for the exposed groups to the reuse of the excreta and are applicable in the use of organic fertilizers in agriculture.