In recent years we have witnessed food scandals involving meat substitution, which drew a lot of attention from the media and consumers. This has resulted in an increased awareness of the risk among food industry professionals and the public, followed by the need for testing, which triggered development of appropriate analytical methods. Molecular biology tools proved to be invaluable in this respect. Assays targeting specific animal proteins [enzyme-linked immunosorbent assay (ELISA)] and DNA markers [polymerase chain reaction (PCR)] are well established today and offered as accredited services by many contract laboratories. This chapter highlights the strengths and weaknesses of both approaches, with particular focus on the technical aspects of PCR-based methods and the challenges associated with the complexity of food samples, the effects of food processing, and the possibilities and limitations of quantitative PCR analysis. The chapter also discusses technical aspects of testing as well as practical considerations and the utility of such assays in the food industry.