Major roads are commonly regarded as migration barriers for most terrestrial animal species. Hazel dormouse, Muscardinus avellanarius, populations in south-eastern Schleswig-Holstein were investigated in order to assess the possible effects of major roads on their genetic variability and genetic structure. A total of 177 samples were collected and analysed, using ten microsatellite loci. Estimates of genetic diversity (expected heterozygosity: 0.48-0.65, allelic richness: 2.9-3.9) were within the range commonly found in this species. No evidence of inbreeding or past bottlenecks was detected. The software structure grouped the samples into five subpopulations. However, this subdivision should be treated with caution, since many individuals with mixed or unclear genetic profiles were found, possibly representing migrants or their offspring. Contrary to the previous assumption that dormice hardly ever cross roads, the present study shows that dormice not only cross even major roads, but also hold close relationships to individuals living on the other side of the motorway. The high number of animals captured within a small area and the relatively low genetic differentiation (FST: 0.142 and 0.105) despite the great distances (33.1 and 25.6 km) along the road, indicate that the roadside shrubs can actually be good habitats for dormice and provide suitable corridors for migration.