AbstractThis chapter describes the principles, components and stepwise protocols for nucleic acid-based methods (e.g. dot-blot hybridization, in situ hybridization and PCR) for the detection and diagnosis of plant viruses and viroids. It also contains information on method optimization and variations, and discusses the advantages and disadvantages of different methods. Further included are practical notes, interpretation of data, notes on pitfalls and trouble shooting. It presents both techniques manageable in modestly equipped laboratories and those requiring more sophisticated facilities.