A parallel survey for the incidence of AI in chicken breeds in Egypt including 12 breeds was performed, together with the screening for the presence of their Mx and MHC alleles. Four years' worth of records of occurrences AI types extending from 2014 to 2017 were used. Also genotyping for the 310 birds under the study using PCR, RFLPs and DNA sequencing was performed. The Baldi (native) chickens were the most affected with all types of AI, especially H5 and H9. In addition, AI was observed in the commercial broilers rather than the layers. Regarding the Mx genotypes, although the only detected genotype was the resistance one (Mx/A+) among the Baldi, Cobb and Ross, they were the most affected with AI. Regarding the MHC haplotypes, neither the B21 (resistance allele to highly pathogenic AI [HPAI]) nor B13 (susceptible allele) was detected among the studied birds. The homozygous genotypes B4/B4 and B11/B11 were the most common, and new MHC alleles were recorded. We recommend recording the names of chicken breeds in AI outbreaks, which will facilitate identification of susceptible breeds in AI outbreaks rather than experimental infection. Further study should be carried out on the most affected breeds with AI to explore their role in the disease epidemiology and whether it is recommended to limit their use during winter, when AI outbreaks occur.