Influenza infections represent a serious threat to human health. Both extrinsic and intrinsic factors determine the severity of influenza disease. The MX dynamin-like GTPase 1 (Mx1) gene has been shown to confer strong resistance to influenza A virus infections in mice. Most laboratory mouse strains, including C57BL/6J, carry nonsense or deletion mutations in Mx1 and thus a non-functional allele, whereas wild-derived mouse strains carry a wild type Mx1 allele. Congenic C57BL/6J (B6-Mx1r/r) mice expressing a wild type allele from the A2G mouse strain are highly resistant to influenza A infections, to both mono- and poly-basic subtypes. Furthermore, in genetic mapping studies, Mx1 was identified as the major resistance locus to influenza infections. Here, we investigated whether the Mx1 protective function is influenced by the genetic background. For this, we generated a congenic mouse strain carrying the A2G wild type Mx1 resistance allele on a DBA/2J background (D2-Mx1r/r). Most remarkably, congenic D2-Mx1r/r mice expressing a functional Mx1 wild type allele are still highly susceptible to H1N1 virus. However, pre-treatment of D2-Mx1r/r mice with interferon α protected them from lethal infections. Our results showed, for the first time, that the presence of an Mx1 wild type allele from A2G as such does not fully protect mice from lethal influenza A virus infections. These observations are also highly relevant for susceptibility to influenza infections in humans.