Abstract The polymerase chain reaction (PCR) is the canonical DNA analysis technique that has enabled the understanding of the complexity of organisms and significantly advanced achievements in the field of biological sciences. Today, the method is still widely used in basic science research, but PCR-based diagnostics are becoming increasingly important in industries such as food and agriculture. This method provides high sensitivity because it requires trace amounts of template DNA to generate enough copies for detection. Using primers specific to the DNA sequence ensures the high specificity of the test. The advantages of the method are time – and cost-effectiveness and reproducibility. PCR-based techniques have found favor in areas where food traceability is important, whether from an economic, legal, health, or religious-cultural point of view. This review outlines the most important aspects in which the PCR method has been successfully applied, namely in the protection of human health by enabling the identification of foodborne pathogens or allergens. Furthermore, the use of PCR in the so-called green criminology, a branch that deals with tracking illegal practices such as food adulteration, compliance with the labeling rules, and detection of food products containing GMO material or other undeclared food ingredients, was also described.