Enterovirus 71 (EV71) is mainly known as a cause of hand-foot-and-mouth disease (HFMD) but sometimes associated with neurological disease, even as fatal brainstem encephalitis. In Europe, EV71 infections are extremely rare, in contrast to the worldwide situation. This is the first report of molecular characterization of an EV71 strain isolated in Europe that had caused neurological disease. The german strain is closest related to sublineage B2 strains isolated in the United States, which where mainly associated with neurological disease. Phylogenetic analysis also showed that the strain must have been imported to Germany several years ago, and continues to circulate since then.