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Background: Aflatoxin B1 is one of dangerous mycotoxins which is produced by Aspergillus fungi. Small intestine especially ileum is important site for absorption and immunity. Aim: To study histological, ultrastructure and immunohistochemical changes by Aflatoxin B1 on ileum of adult male albino rat and the possible protective effect of sodium selenite. Materials and Methods: Forty adult male albino rats were used, they were divided into four groups, control group (GI), sodium selenite group (GII), Aflatoxin B1 group (GIII), Aflatoxin B1 and sodium selenite group (GIV). Sections were stained by H&E, Mallory, Alcain blue and proliferating cell nuclear antigen (PCNA). Ultrathin sections were prepared for electron microscopic study. Morphometric study for different measurement in ileum were done. Results: Aflatoxin group show marked destruction, disorganization of most villi and crypts, necrosis and vacuolation of covering and lining cells. Hemorrhage, hyalinization and necrosis in submucosa and muscle layers with heavy lymphocytic infiltration are seen. Alcain blue stain show significant decrease in intensity. Goblet cells and PCNA + ve cells reveal significant decrease in their numbers. All sections show marked improvement with selenite treatment, ultrastructure changes are in harmony to light microscope findings. Conclusion: Aflatoxin B1 has destructive histopathological changes on all layers of ileum and sodium selenite has protective effect against this damage.