Molecular detection methods based on PCR (polymerase chain reaction) are widely used in the rapid detection of food-borne pathogens. However, in practical applications pretreatment method is also a critical step in rapid detection except the optimization of PCR. In this review, the pretreatment methods (including the centrifugation, membrane filtration, magnetic separation) for PCR detection of food-borne pathogens were systematically summeried. In particular, the magnetic separation was emphatically reviewed in the PCR detection of food-borne pathogens.