Foodborne pathogens comprise microorganisms such as viruses, bacteria and parasites that can be transmitted by food and affect public health worldwide. The most common viruses transmitted via food are hepatitis A virus and Norwalk-like caliciviruses. Also, the most common bacteria involved in foodborne illnesses are Campylobacter jejuni, Clostridium perfringens, Salmonella spp, Escherichia coli O157:H7 and the most important parasites that can cause these conditions are Giardia duodenalis, Cryptosporidium parvum, Cyclospora cayetanensis, Toxoplasma gondii, Trichinella spiralis, Taenia saginata and/or solium, Entamoeba histolytica, Anisakis spp. and Diphyllobothrium spp. Because of their eventual small number in the sample, their detection and identification is not always easy. On the other hand, conventional methods like cultures are almost labor intensive, time consuming and costly. Recently, molecular techniques have been developed for rapid, sensitive and specific identification. The most common molecular methods are polymerase chain reaction (PCR)-based techniques. In this article, the sensitive and specific molecular tests for routine detection and identification of foodborne pathogens are reviewed.