Hypothesis universally accepted as the most likely route of infection with ESB appeared due to the consume of the animal by-products which are not intended for human consumption that contained prion protein derivative - infected led to ban the feeding of farmed animals with processed animal protein (PAP) that focused primarily feed for ruminants and later expanded to all feed for all farm animals. Entry into force of the ban on the use of the processed animal proteins (PAP) in feed for farmed animals and especially in ruminants is considered an important measure of prophylaxis to prevent BSE so the identification and the microscopic estimation of the constituents of animal origin became the official method and mandatory in all Member States. The microscopic analysis depends upon the identification of the hsitological characters macro-and microscopic structural of the processed animal tissue added in feed mixtures.To identify the microscopic animal constituents, some technical conditions are essential: optical microscope, stereo microscope, high-density solvent (chloroform or tetrachloroethane) clarifying agents (phenol-glycerol, paraffin), microscope with digital visual images support as decision support . The method allows the identification of bone fragments, muscle tissue, hair, feathers, shell fragments and plant and mineral components. Nowadays four different approaches are applied to control the compliance on the prohibition of feeding with PAP: microscopic analysis, immunological analysis, infrared spectroscopy and microscopy (NIR), polymerization chain reaction (PCR). In this stage, the microscopic method is the only method validated and able to identify the nature of the animal in feed components with detection limit of <0.1%, but it cannot accurately detect the species of origin.