Despite the long-term study of the house mouse hybrid zone in Europe knowledge of its course in some areas is still rather vague. Comparisons of different portions of the zone showed some common patterns, however, several discordances were also revealed, the most remarkable being introgression of the Y chromosome. We sampled mice along the presumed course of the secondary contact zone between two subspecies, Mus musculus musculus and M. m. domesticus, from Schleswig-Holstein to southern Bavaria, in order to localize more precisely its position. A second aim was to reveal whether introgression shows some general rules obscured until now by studies of geographically isolated transects of the zone. We employed maternally (mtDNA), paternally (Y), and biparentally inherited markers and related their introgression patterns to the hybrid index (HI) based on five X-linked loci. While transition of autosomal loci across the zone was congruent with changes in HI, mtDNA showed bidirectional introgression with alien alleles occurring far behind the zone. Finally, the Y chromosome displayed asymmetric unidirectional introgression of the musculus type into domesticus background. We discuss evolutionary forces shaping these patterns.