In organic farming systems the focus is on prevention with regards to plant protection. To follow the rules of Good Agricultural Practice one is able to avoid serious yield losses; if it is not possible the use of allowed materials are permitted. Organic farmers have less material to protect their plants so it is necessary to find effective potential materials. Bacterial and fungal diseases of tomato and pepper can cause serious losses in yield. Different materials were tested against some plant pathogen bacterial (Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato, Xanthomonas campestris pv. vesicatoria and fungal (Phytoptora infestans, Rhizoctonia solani, Sclerotinia sclerotium) strains in order to find potential materials in the field of organic seed treatment. In vitro trials have shown that vinegar, cider vinegar, red wine vinegar, white wine vinegar, cinnamon and thyme oil have inhibiting effect against the causative agent of bacteria and fungi. Germination test has shown that examined vinegar types do not decrease germination ability if the concentration is low, but in higher (more than 5%) concentration it ruins the germination ability. Even in 0,5% concentration of red — and white vine vinegar have good effect on germination capacity.