Facing the ongoing decline in garden dormice (Eliomys quercinus) in large parts of Europe, data about genetic diversity, weight, size, and parasite burden were collected from live individuals (n = 156) from Hesse and Rhineland-Palatinate, Germany. Blood was collected under Isoflurane-oxygen-anaesthesia from the anterior vena cava or jugular vein, respectively. Sex, weight, tibiotarsal and tail length of all animals were recorded. Genetic analysis (n = 64) using hair samples, viral examinations of oral, ocular and anal swabs (n = 156) and parasitological examination of faecal samples (n = 57) were performed. Genetic analysis of mitochondrial DNA revealed three haplotypes in the study area (WE4, WE4-3, WE5). Microsatellite analysis demonstrated a comparably high genetic diversity with 66 % overlap of alleles, a low genetic distance (D_Jost 5.6 %) and a low index of differentiation (F_ST = 0.02) between individuals from Hesse and Rhineland-Palatinate. All swab samples were negative for Borna disease virus. In 47 % of the faecal samples Entamoeba sp. cysts, Eimeria sp. oocysts, and eggs of trematodes, cestodes (Hymenolepis spp.) and nematodes (Capillaria spp., Strongylida) were detected. To our knowledge, this is the first report of inhalation anaesthesia, clinical examination, blood collection and assessment of Borna disease virus in living garden dormice.