Rhizomania of sugar beet caused by the Beet necrotic yellow vein virus (BNYVV) and transmitted by Polymyxa betae leads to great losses of yield in sugar beet production worldwide. The virus is multiplying in the sugar beet and its roots are finally enclosed in P. betae sporosori and released into the soil during decomposing. Virus and vector sporosori remain infectious in the soil for years. Setting free sporosori und BNYVV into the environment during sugar production and deposing of contaminated waste implies a phytosanitary risk for spreading rhizomania. Fermentation of plant residues in biogas plants could possibly lead to inactivation of P. betae and/or BNYVV. Within a research project, conducted at the Bavarian State Research Center for Agriculture (LfL), the persistence of different pathogens — including P. betae and BNYVV — during biogas fermentation was studied to evaluate the hygienisation potential of the biogas process and to assess the risk of spreading pathogens with the fermentation residues. To investigate BNYVV tenacity, infected rootlets of sugar beet plantlets were incubated at 38°C and 55°C in 36 l-continuous fermenters up to 36 days and analyzed by ELISA directly after fermentation. In addition, to check the infectivity of the vector/virus complex a bioassay was performed. When fermented at 38°C, BNYVV could be detected by ELISA in the rootlets for up to 36 days, but only during the first 4–8 days of incubation infectivity of virus and/or vector were retained. Compared with incubation at 38°C, incubation at 55°C led to an enhanced degradation of BNYVV and accelerated loss of viral and/or vector infectivity: BNYVV antigen concentration was dramatically reduced and reached a minimum after 3 weeks of incubation. Viral and/or vector infectivity were lost very fast already during the first 4 days of incubation in the fermenter. It can be assumed that biogas fermentation under thermophilic but also mesophilic conditions leads to a relatively fast inactivation of BNYVV and/or its vector P. betae. At least with respect to rhizomania, widely harmless fermentation residues should be produced if the retention time in the fermenter at temperatures between 38°C and 55°C is at least 1 week. But nevertheless, for a full assessment of the phytosanitary risk additional studies are required.