Background: Candidatus Phytoplasma ulmi is the causative agent of elm yellows and has been categorised in the European Union as a quarantine pathogen in the past. For central and northern European countries, information on the occurrence and distribution of the pathogen and its impact on elms is scarce, so a survey of native elm trees has been conducted in Germany. Results: About 6,500 samples in total, from Ulmus minor , Ulmus laevis and Ulmus glabra , were collected nationwide. Phytoplasma detection was performed by applying a universal 16Sr DNA-based real-time PCR assay and a novel Ca . P. ulmi species-specific real-time PCR assay targeting the 16S-23S spacer region. Both assays revealed that 28% of the samples were infected by Ca . P. ulmi, but infection rates of the elm species and regional incidences differed. The infection of trees is not correlated to disease-specific symptoms. The survey identified a regional disparity of infection which was high in east, south and central Germany, whereas only a few infected sites were found in the western and northern parts of the country. No correlation was apparent between altitude level and the prevalence of infection. First insights into the monitoring of the seasonal titre of Ca . P. ulmi in an infected tree by real-time PCR revealed high colonisation in all parts of the tree throughout the year. Conclusions: Ca . P. ulmi-infection is widely present in elms in Germany. The rare occurrence of symptoms indicates either a high degree of tolerance in elm populations or a low virulence of pathogen strains enabling high infection rates in a long-living host.