The Panel on Plant Health performed a pest categorisation of the fungus Synchytrium endobioticum, the causal agent of potato wart disease, for the European Union (EU). The identity of the pest is well established and reliable methods exist for its detection and identification. S. endobioticum is present in most continents. The pest is listed in Annex IAII of Directive 2000/29/EC and is present with a restricted and fragmentary distribution in the EU. The major host is Solanum tuberosum (potato), but in Mexico, the pest also affects wild Solanum spp. S. endobioticum could potentially enter the EU through multiple pathways associated with soil as substrate for non‐host plants, contaminant or commodity. The presence of the pest in 16 EU Member States characterised by different climatic conditions suggests that it could establish in the rest of the EU. The disease induces the formation of warts on potato tubers, stolons and stem bases reducing plant growth and yield and making tubers unmarketable. Additional losses may occur during storage. The only available strategy to control the disease and prevent it from spreading is the application of strict phytosanitary measures and the cultivation of potato varieties resistant to the pathotype(s) present in the infested field(s). Specific phytosanitary measures exist (Council Directive 69/464/EEC) for the control of potato wart disease in the EU. The main uncertainties refer to the distribution and host range of the pest, and the importance of some pathways of entry. S. endobioticum meets all the criteria assessed by EFSA for consideration as potential Union quarantine pest. The criteria for considering S. endobioticum as a potential Union regulated non‐quarantine pest are not met since, in addition to potato seed tubers, soil (as commodity, substrate or contaminant) and ware potato tubers are major means of spread.