This study aimed to evaluate the effect of long term administration of Nigella sativa seed as an herbal immunomodulatory agent on histological features of caecal tonsils and bursa of Fabricius in broiler chickens. Fifty, one-day old chick were randomly divided into five equal groups and fed with diets containing  0, 0.5, 1, 1.5, and 2% of N. sativa seedsfor 45 days. Then birds were slaughtered and 6μm-thick cross sections were made from caecal tonsils and bursa of Fabricius and stained with hematoxylin and eosin. Villus height and villus basal width, nodular unit width and height, follicular width and muscular layer width in caecal tonsils as well as height of plicae, follicular width, thickness of follicular cortex and medulla in bursa were determined. In addition, number of follicles in each plica in bursa of Fabricius and number of follicles per nodular unit in caecal tonsils were determined under light microscope. The results showed a change in all histomorphometric parameters of caecal tonsils due to N. sativa administration which followed a dose-dependent pattern in most cases. Villus height, nodular unit width and muscular layer width were decreased while other parameters increased as compared to control. Although all parameters in bursa increased due to N. sativa seed administration, plica height was the only parameter which showed a dose-dependent change. In conclusion, dietary inclusion of N .sativa especially at 2% dose, can improve immune structures of both bursa of Fabricius and caecal tonsils of broilers.