Most agricultural wastes are valuable resources that should be recycled and used for industrial purposes and for energy recovery. If unsuitably handled and managed, agricultural wastes become an environmental problem and a hazard for human and animal health. The management of agricultural wastes is considered as an important target in the global waste management strategy. Any kind of waste can become a hazard factor for humans, animals, and vegetation, if its concentration in the environment is excessive. Water quality is affected if manure runs into water streams as a result of inappropriate and excessive land application, spillage, overflow, or deliberate dumping. The nutrients and organic matter contained in manure can pollute the ground water by leaching or by runoff when manure is applied at rates exceeding crop fertilizer requirements. In such cases, arrangements should be made to move excess manure to other cropland, or to use it for other purposes. The wastes of agricultural origin can be contaminated with crop and animal disease-causing organisms and chemicals and with chemical and physical contaminants. Some of the main issues related to optimum utilization of agricultural wastes refer, therefore, to the control of chemical pollutants (organic and inorganic), breaking the chain of diseases transmission by the inactivation of pathogens and other biological hazards, and the removal of physical impurities.