The use of manure as a fertilizer in agriculture includes the risk of spreading pathogenic infectious agents to the environment, to animals and humans. The treatment of manure can help avoid or reduce these risks. Even if the treatment is dominated by economic considerations such as biogas production, ammonia stripping or phosphorous precipitation, the hygienic aspect should be kept in mind. Otherwise, new infection chains may be established by the use of insufficiently treated manure by-products such as fertilizers still containing infective pathogens. Treatment plants should use a concept according to HACCP principles that includes hazard analysis, risk assessment, the determination of process relevant CCPs and the validation of the process by determining the hygienizing efficiency using representative test organisms as well as microbial end product supervision. Treatment methods can be divided into physical, chemical and microbiological treatment, sometimes used in combination. For economical reasons, only composting or anaerobic treatment (biogas) or, to a minor extent, aerobic thermophilic stabilization (ATS) are used as routine preventive measures on a farm level. In cases of outbreaks of notifiable diseases both physical and chemical treatment of manure can lead to reliable disinfected/pasteurised end products which can be used in agriculture without long-lasting risks for soil fertility or the environment.