The presence of pathogens in animal manure depends on several factors such as, for example, the species, age, type of power supply, state of health, methods and times of storage, treatments administered. Currently there are no specific requirements for the minimum sanitary standards of livestock manure to be used in agriculture, or even of the digestate resulting from anaerobic digestion, such as cattle slurry and plant matrices (e.g. maize). While there are some indications for products fermented aerobically (compost deriving also from manure) and the sludge resulting from wastewater treatment and intended for use as fertilizers. In this paper we sum up the information given in the scientific literature on the viability of some microorganisms and on the effects of the anaerobic digestion of livestock manure and plant matter, such as maize, on the microbial concentrations.