Plant pathogens present a serious threat to seedling establishment and the potential for plant disease epidemics under greenhouse conditions is great. Hence, pathogen exclusion by detection and elimination of infested seedlots remains a requisite tactic for seedling production and disease management. Unfortunately, the numbers of contaminated seed within a lot may be low and infested seed may be asymptomatic making their detection difficult. To address these issues seed detection assays have been developed, but many of them have shortcomings that reduce their effectiveness. Examples of frequently used seed assays include visual examination, selective media, seedling grow-out and serological assays which, while appropriate for some pathogens, often display inadequate levels of sensitivity and specificity. Recently, the polymerase chain reaction (PCR) has emerged as a tool for detecting microorganisms in many diverse environments. Thus far, it is clear that DNA-based detection systems exhibit higher levels sensitivity than conventional techniques. Unfortunately, PCR-based seed tests require the extraction of PCR-quality DNA from target organisms in backgrounds of saprophytic organisms and inhibitory seed-derived compounds. The inability to efficiently extract PCR-quality DNA from seeds has restricted the acceptance and application of PCR for seed detection. To overcome these limitations several modified PCR protocols have been developed including selective target colony enrichment followed by PCR (BIO-PCR) and immunomagnetic separation and PCR. These techniques seek to selectively concentrate or increase target organism populations to enhance detection and have been successfully applied for detecting bacteria in seed. Other techniques with great potential for rapid detection of seedborne pathogens include magnetic capture hybridization and PCR, and DNA-chip technology. Ultimately, PCR will be available for the detection of all seedborne pathogens and may supersede conventional detection methods.