Abstract: Aflatoxins are a natural secondary product produced on many storage agricultural commodities which contaminated with a number of toxic fungi particularly A. floviu s and A. parasiticus because of the prevailing climatic conditions as well as faulty and unhygienic storage method used. The presence of aflatoxins in animal feeds cause a major problem and great losses and toxicity to domesticated animals and poultry , and considered to be a potential health hazard to human health. Studies of the histopathological changes that results from effects of aflatoxin BI on the cells of the immune system have not been taken by consideration, the present study designed to reveal the effects of this mycotoxin. on the thymus gland and spleen that considered as a major organs of the immune system. Results of the present research can be summarized as follows: 1-The capability of 23 isolates from (A.flavus and A.parasiticus) were examined for the aflatoxins production, it appeared that only 13 isolates were aflatoxin BI producer Awhile the others were not producer of aflatoxins. The amount of aflatoxin BI produced by toxigenic fungi of (A.flavus and A.parasiticus) on maize substrate was ranged between (2.129-600.02 ppb) . The strain N1 (A. parasiticus) gave the highest aflatoxin BI roducer (600.02 ppb) and used in all experiments, while the strain N12 (A.parasiticus) gave the lowest aflatoxin B1 production The best temperature suitable for high aflatoxin BI production in maize substrate was 25°C . 4- The use of crude aflatoxin BI or the diet contaminated with spores of isolate NI (A.parasiticus) caused the increasing in the relative body weisht , atrophy of thymus gland and swelling of the spleen , in addition to increasing of water consumption, inclination of the treated rats to retirement, bristling up of hair with food refusal. 5- The histopathological study involved the major organs of the immunity (thymus gland and spleen). After ten day s of the treatment, the light microscopic examination showed the decreasing in (cortex / medulla) ratio, but the decreasing in (cortex/ medulla) ratio in thymus gland of rats treated with crude aflatoxin B1 was more than the decreasing of (cortex/medulla) ratio in thymus gland of rats treated with the contaminated diet. In spleen, the white pulp and red pulp in splenic tissue of rats treated with contaminated diet could not be differentiated from, each others due to the damage in the marginal zone , while the spleen of rats treated with crude aflatoxin B! was characterized with a marked degeneration of the white pulp and red pulp and the congestion due to the aggregation of red blood cells in the blood vessels. 6-The ultrastructure study of thymus gland and spleen by SEM and TEM revealed changes in all treated rats, these changes appeared in the surface morphology and in the microvilli which have the important role in the cell movement and phagocytic process that important in the immunity, also these changes involved the nucle us, the cellular membrane, the cytoplasm and the mitochondria. In spleen , the effect of aflatoxin BI was noticed on the same contents of the cells mentioned above in addition to the changes of ribosomes. white pulp and red pulp.