Many plants viruses and viroids are reported to be pollen and seed transmitted. Their presence in several fruit trees varietal collections used as source materials for genetic breeding makes it necessary to establish appropriate protocols to avoid their diffusion with propagating material. Although sometimes mandatory by law, the destruction of infected mother plants might entail the irretrievable loss of valuable genetic material. The genetic uniqueness of the infected material would make its sanitation imperative, to avoid compromising the breeding programme. However, during sanitation, germplasm has to be kept in isolation. Available diagnostic methods are sensitive and reliable, and their continuous evolution leads to consider further refinement and simplifications for the future. These methods have already greatly favoured fruit trees nursery production, allowing a continuous monitoring of plant material throughout the breeding process. A better co-operation between complementary scientific disciplines is highly desirable in this field also.