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The experiences of a veterinary research and diagnostic laboratory are summarized on the development and application of the PCR to diagnose a wide range of viral diseases in animals. The group started the routine diagnostic application of the PCR as early as 1988 and today a total of 35 nested PCR assays are in routine use for the detection of 15 DNA and 20 RNA viruses. Special tools and laboratory practice were applied to avoid falsepositive results, while false-negatives are avoided by internal controls (mimics). At present, the classical nested PCR methods are being replaced by real-time TaqManTM and molecular beaconTM assays and the multiplex real-time PCR detection of viruses is also under development. By direct sequencing of the PCR products, phylogeny studies are performed and molecular epizootiology results are provided for rapid and exact identification of virus variants. Molecular epizootiology also contributes to trace the routes of virus spreading on large geographic areas. Recently, large efforts have been made to follow the recommendations of Office International des Epizooties for the standardization and international harmonization of the molecular diagnostic assays.