The objective of the research was to determine the efficiency of cold plasma (He+Air) pre-sowing stimulation of seeds of onion (exposure time: 60, 120, 240 and 480 seconds) in the prevention of the occurrence of fungal pathogens of onion and health of seeds. The experiment was conducted on the Petri dishes with mineral medium in laboratory of Plant Protection Department. The use of cold plasma reduced the severity of the diseases in all combinations. Better results were obtained for seeds treated by plasma during 480 s. Seeds were settled mainly by Alernaria alternata, Penicillium spp., Trichoderma harzianum and Fusarium oxysporum. The observations suggest that there is a possibility of onion seed treatment for production under conditions of organic cropping system without chemical pesticides.