Potato wart disease, caused by the chytridiomycete Synchytrium endobioticum, was first introduced into Europe in the late 19th century. It spread quickly, and today is reported in 15 European countries. Initially, only one pathotype was found, and the disease was efficiently controlled using resistant cultivars. In 1941, however, formerly resistant cultivars showed wart formation in the field simultaneously in Germany and South Bohemia (Czech Republic), indicating the occurrence of new pathotypes. New pathotypes have since been reported from Germany, The Netherlands, Czech Republic, Ukraine and Canada. Today the pathogen is present in The Netherlands (only in fields for ware and starch potatoes) but restricted to two demarcated areas and subject to official control. Outside these areas, the pathogen is absent. For pathotyping, different countries have used different sets of differential cultivars, and the usual system of numerical coding of pathotypes has not been consistently followed. In this review we propose a new standardised code to be used for the 43 pathotypes currently known and described in Europe. The code is a combination of a numerical and letter code, combining the two terminologies used by former West and East Germany, respectively. We also plead for harmonisation in the choice of differential cultivars used for pathotype identification. The set of differentials described in the international standard for diagnosis of S. endobioticum issued by the European and Mediterranean Plant Protection Organisation (EPPO), should serve as a basis. Through close collaboration of European countries dealing with new pathotypes of potato wart disease, a final agreed upon set of differentials, combined with a set of reference isolates, should ultimately be established, allowing a clear distinction between the most important pathotypes occurring in Europe.