Defensins of birds belong to the large family of antimicrobial peptides that are key components of mucosal innate immunity. Gene expression of two major avian defensins (AvBD1 and AvBD2) in the chicken intestinal tissue is linked to the host protection against Salmonella colonisation. These antimicrobial peptides can be produced by granulocytes and by epithelial cells. They can be purified from chicken bone marrow and are active against a large panel of Gram+ and Gram- bacterial species. While intestinal expression of AvBD1 and AvBD2 can be observed at birth, how it evolves with age remains unclear. In order to assess the influence of the gut microbiota, we compared defensins genes expression profiles in conventional and axenic chicken intestinal tissues during the first two weeks of life. Kinetics of expression of AvBD1 and AvBD2 were different, independently of the microbiological status of the chicken gut. Interestingly, AvBDs expression level appeared lower in the small intestine of axenic chicken by comparison to conventional birds. The presence of a flora seems thus to positively influence the level of expression of AvBDs in the chicken gut. Future work will be devoted to the identification of commensal bacterial species that are beneficial for these antimicrobial peptides expression.