Grapevine and fruit trees have a lot of pathogens including viruses and viroids. Because conventional technologies of protection against these can not be used effectively, the only solution is prevention and screening of plants used for propagation. However traditional screening methods are expensive, not sensitive enough, and often labor-intensive. Our new method is essentially different. We use high-throughput sequencing of viral smallRNAs, detecting all viruses and viroids in the plant tissues without any prior knowledge of virus sequence, hence we can identify both known and unknown pathogens.