The output of fermentation end products are often considered to be problematic, when weed seeds have been inserted at biogas plants. Regarding the level of risk at the output of fermentation end products with weed seeds you will find opposing opinions. For the evaluation of the sanitation degree of problem weed seeds (Avena fatua, Rumex obtusifolius, Atriplex patula, Bromus sp., Galium aparine, Amaranthus sp., Ely-trigia repens, Chenopodium album, Echinochloa crus-galli, Polygonum lapathifolium, Ambrosia artemisiifolia, Capsella bursa-pastoris, Stellaria media) and agricultural crop species (Zea mays, Trifolium pratense, Triticum aestivum) the germination was tested at varying dwell times and different temperatures in a biogas fermenter and under laboratory conditions. The weed species Avena fatua, Rumex obtusifolius, Atriplex patula, Bromus sp., Galium aparine, Amaranthus sp., Elytrigia repens, Echinochloa crus-galli, Polygonum lapathi-folium, Ambrosia artemisiifolia, Capsella bursa-pastoris, Stellaria media and agricultural crop species Zea mays, Trifolium pratense, Triticum aestivum showed a total loss of germination after a short period in the fermentation substrate. The germination level of all species except for Chenopodium album was 0% after one week at about 35C (mesophilic ambiance), nevertheless after three weeks of exposure Cheno-podium seeds were no longer germinable. The deterioration of the germination po-tential was even faster at a temperature of about 50C in the thermophilic envi-ronment. Laboratory tests using Tetrazolium confirmed the total loss of viability, only hard seeds of clover and alfalfa species need a differentiated view. The sanitation process depends on different parameters, like pH-value, microor-ganism activity, anaerobic ambiance, mechanical influences, noxious gas concen-tration as well as the substrate temperature and the dwell time of the seeds in the fermenter. The dissemination risk of problem weed species by fermentation end prod-ucts can be classified as extremely low. Common practice shows that the time of exposure is normally longer and is mostly followed by retention in the final storage for several weeks almost excludes the whole risk of output from germinable seeds.