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Lyme borreliosis is currently the most frequent tick-transmitted zoonosis in the northern hemisphere. Germany and other European countries are regarded as highly endemic areas; therefore the burden of disease and consequently the costs for the health systems are considered to be high. This report summarises the results of an interdisciplinary workshop on Lyme borreliosis which aimed to identify research deficits and to prioritise areas which need to be addressed. Research needs have been recognised for different areas: diagnosis, epidemiology, immunology, clinics, ecology and health services research. Examples of research areas which have priority are the standardisation of diagnostic tests, the development of markers to detect an active infection, the improvement of the epidemiological database and the analysis of the burden of disease.