In this study, the evolutionary forces acting on four wild populations of the house mouse Mus musculus were analysed by high-density SNP-genotyping arrays. Statistical analysis showed evidence for selective sweeps at rare and newly mutated alleles, indicating positive selection. Furthermore, positive selection was shown to result in a high percentage of introgression, resulting in the permanent incorporation of genetic material from one subspecies to another. Thus, introgression of haplotypes has a larger role in adaptive processes than was previously thought.