Through evolution, plants produce seeds with variation in speed of germination and, for instance, dormancy to spread the risk of germinating in the wrong season. Although domestication and breeding has created crops with more rapid germinating seeds, compared with their wild relatives, for many crops the variation in performance is such that upgrading and seed treatments are needed to create starting materials for commercial crop production. Measures are needed during the production itself, and during harvesting, cleaning and drying. In this chapter we will report on various factors that influence organic seed quality and availability, on methods for seed sorting, upgrading and storage, on methods of seed sanitation that are applicable for organic seeds and on seed certification systems. We will point on research that has been performed in the past and resulted in commercially available methods for upgrading of seed quality and on promising new research lines.