Many different plant pathogens can be seed transmitted. In a world of global trade seeds infected with different plant pests are a potential risk. Seed health testing is important to prevent the spread of diseases. For the detection of these seed transmitted pests many methods are available e.g. ELISA, IF, dilution plating, PCR and real-time PCR. This chapter discusses several methods for seed health testing. It also evaluates the use of NGS sequencing for the detection of the most important seed transmitted pathogens in tomato: Clavibacter michiganensis subsp. michiganensis, Xanthomonas euvesicatoria, X. perforans, X. vesicatoria and X. gardneri, Pseudomonas syringae pv. tomato, Pepino Mosaic Virus and Potato spindle tuber viroid. These methods are compared with TaqMan PCR methods.