The basic principles for the development of organic agriculture has been prescribed by the International Federation of Organic Agriculture Movements -IFOAM and the European Union (Commission Regulation No 209/91), on whose standards EU regulations are founded. The field of organic production at the international level and issues of seeds and planting material are regulated by the IFOAM Basic Standards 2002, which stipulates that seed and planting material used in organic agriculture has to be produced in line with the regulations applicable to organic crops. Unlike the conventional seed production, in organic seed production, there is a higher risk of contamination with pathogens, i.e. seedborne diseases. The aim of this study was to point out the existing methods of seed treatments in the organic production system in order to obtain healthy seeds. Seed-borne pathogens, including bacteria, fungi, viruses and viroids, are responsible for disease recurrence in subsequent cycles of seed multiplication and spread of diseases in new geographic regions. According to various authors, there are several classifications of treatments including physical treatments, application of natural compounds, such as plant extracts and oils, use of inorganic natural products and biological control (use antagonistic microorganisms). In order to overcome various pathogens different biocontrol strategies should be developed. Microorganisms can be used in diverse crop protection practices, i.e. several seed treatments can facilitate high levels of both disease control and production yield.