Avian influenza is a serious threat to the poultry industry and, as the potential source of a human pandemic virus, to public health. Different Mx alleles have been reported to confer resistance or susceptibility to influenza virus replication, and so knowledge of their frequencies is important when considering the potential for improvement of modern commercial flocks. We analysed a range of chicken lines and ancestral breeds for the relevant Mx codon that confers resistance or susceptibility to influenza virus replication. We confirmed the high frequency of the susceptibility allele in contemporary meat-type (broiler) birds compared to egg-laying strains and found this difference is present already in ancestral breeds. We sequenced full-length complementary DNA (cDNA) and noted additional substitutions, which may be associated with the resistance haplotypes. High frequencies of the susceptibility allele could be readily reduced by modern breeding techniques.