We collected samples from live-trapped bank voles at Kalvs Mosse, east of Lund, southern Sweden in 2009. The MHC class II DQB genotype (MyglDQB) were screened in 12 families, mothers and pups. The data set contains 41 columns (36 of which are MyglDQB-alleles). Seven of the ten population haplotypes are found in the mothers and these maternal haplotypes are color coded; in color if the haplotype is common (>5%) and in grey if rare (<5%). The three remaining population haplotypes can be inferred by paternal haplotypes but are only inferred based on common (>5%) haplotypes in main data set (indicated in colored text). Detailed information about each column can be found in the published manuscript.