BACKGROUND: The trachea is the main air passages which is important for taxonomic reasons. The structure of trachea varies considerably in different avian species. OBJECTIVES: This study has been carried out in order to determine the histological and histochemical structure of the trachea in ostriches. METHODS: Sixteen tracheas of 8 female and 8 male nine-month-old healthy blue-necked African ostriches in slaughterhouse of Isfahan were selected. Each trachea divided into cranial, middle and caudal portions and fixed in 10% neutral buffered formalin. Tissues sections were stained with H&E and special stains included Masson’s trichrome, Verhoeff’s, Foot’s, Van Gieson’s, Periodic acid-Schiff, and Alcian blue. RESULTS: The trachea of blue-neck ostriches was composed of tunica mucosa-submucosa, cartilaginous, muscular and serosa. The epithelium was ciliated pseudostratified columnar contained simple alveolar goblet mucous glands. These glands reacted negatively to Periodic acid-Schiff but positively to Alcian blue. The propria-submucosa was composed of dense connective tissue. The muscularis mucosa was absent. Tunica cartilaginous and muscular was made up of sternotrachealis muscle and cartilaginous rings. The rings were only composed of hyaline cartilage. There is no osseous tissue in the tracheal rings. Tunica serosa was composed of loose tissue contained parasympathetic ganglia, adipose tissues, vessels, and all the connective fibers. Three final cartilage rings were shaped tympanum of the syrinx. The histological structure of the trachea showed no significant differences between the male and female ostriches. Except for the decreased number of mucous glands in caudal portion of the trachea, the histological structures of the trachea showed no considerably differences among various portions. CONCLUSIONS: Based on this study, it can be concluded that although the histological and histochemical structure of the trachea in ostrich was similar to those of some other species, but that there were also some differences.