There is mounting evidence that some European temperate species did not respond to the last (Weichselian) glaciation by simply shifting their distributions to the Mediterranean region but also survived at higher latitudes previously considered inhospitable. However, it remains to be determined to what extent such high-latitude glacial refugia contributed to post-glacial colonization of Europe. The bank vole Myodes glareolus apparently survived in a high-latitude glacial refugium in the Carpathian Mountains. Here, we used 144 new mitochondrial DNA sequences (largely obtained from museum skins), together with relevant previous data, to investigate whether the phylogeography of bank voles currently living in deglaciated areas north of the Carpathians reflects colonization from this or other refugia. Phylogenetic reconstruction resolved the newly identified haplotypes into three major clades. The majority of voles sampled in Poland carried haplotypes of the Carpathian clade, previously only known from the Carpathians and their immediate vicinity. Voles from eastern Poland and northern Germany carried haplotypes of the Eastern clade, also found in eastern Europe and Siberia, and six voles from scattered localities carried haplotypes of the Western clade, which has a west European distribution. Therefore, the results suggest the contribution of multiple glacial refugia. However, the occurrence of the Carpathian clade over a large area north of the Carpathians up to the Baltic Sea coast indicates a particular importance of the Carpathian refugium. Thus, a substantial involvement of a high-latitude refugium in the post-glacial colonization of Europe by bank voles is inferred. Likely as the consequence of the high-latitude survival, the Carpathian clade lacks evidence of the severe demographic bottleneck during the Last Glacial Maximum that is observed in the Eastern clade. The contact zone between the expanding populations of the Carpathian and Eastern clades coincides with subdivisions in other species and may represent a new post-glacial suture zone.