Mx1 (Myxovirus (Influenza virus) resistance 1, interferon-inducible protein p78) gene has been implicated in the resistance to a wide range of RNA viruses including influenza A in several species such as Sus scrofa. In the present study a 28-bp deletion in exon 14 of the Mx1 gene has been identified in Iberian domestic pigs but not in other domestic breeds neither in wild boars. The mutation produces a frameshift giving a protein with 6 amino acid substitutions and the extension of the C-terminal region with additional 20 amino acids with respect to the wild type MX1 protein. The new allelic polymorphism affects the antiviral domain of the MX1 protein and therefore might impact its anti-influenza virus activity. It has been demonstrated that polymorphisms in the Mx1 murine locus, affect the survival rate of mice upon experimental infection with influenza virus. It might be possible to improve the innate resistance of pigs to influenza virus infection by determining the porcine Mx1 alleles with more potent antiviral activity and genetically selecting animals bearing such alleles.