Efficiency of regeneration of mechanically injured skeletal muscle is more pronounced in SJL/J mice, as compared to other laboratory strains in which regenerative properties of skeletal muscle are uniformly poor. Previously, we postulated that a small number of genes might differ between SJL/J and other mouse strains, and would be responsible for this variation in the efficiency of skeletal muscle regeneration. The results of initial experiments demonstrated that SJL/J mice have a unique form of the myogenic gene, Myo-D1, which partly influences efficiency of skeletal muscle repair, and that other genes were also involved. To identify other candidate genes, differences were sought within the myogenic paired box/homeobox-containing gene Pax7 between SJL/J and other laboratory mouse strains. Southern blotting indicated that SJL/J, Quackenbush and DDO mice share a Pax7/TaqI RFLP which differs from all other laboratory strains tested. This RFLP is most likely due to sequence differences within the homeobox of a Pax7-like gene. In vivo studies revealed that Quackenbush and DDO mice also share the same regenerative properties of mechanically damaged skeletal muscle as SJL/J mice. Since Quackenbush and DDO mice lack the SJL/J type of Myo-D1, and DDO belong to a different mouse sub-species, these studies suggest that structural alterations in the homeobox of a Pax7-like gene may be implicated in the effectiveness of renewal of damaged skeletal muscle of the limb in the mature animal.