The aim of the study was to present the results of comparative evaluation of the usefulness of PCR and microscopic methods for the detection of Processed Animal Protein (PAP) in feedingstuffs. In the validation study, the limit of the detection for PCR was determined on 0.05% for beef, 0.1% for pork and 0.2% for poultry meat and bone meal (MBM). Among 62 doubtful samples of feedingstuffs examined by microscopic method 41 (66.13%) were found as positive. Based on the results obtained with the use of the microscopic and PCR methods it is possible to state that the molecular biology methods can, at present, be used as a supplementary method in PAP detection