Abstract: Infectious Bursal disease is one of the important diseases of poultry. This disease caused severe economical losses such as mortality, retardation of growth and immunosuppressant, especially at 3-6 weeks chickens. Histopathologic lesions were appeared in Cecal tonsil and other lymphoid tissues. Destruction of infected lymphocytes with virus and peripheral cells and depletion of lymphocytes in Cecal tonsil were caused by necrosis and apoptosis. In this study, 50 SPF 28 days olds chickens were divided in to tow groups (control and experimental) with 25 chickens in each group. The experimental group was infected orally by 106EID50 in 1 mL of IR499 (IRAN499) virus (vvIBDV) in control group physiological saline solution was used. At 4th days post infection, all birds were sacrificed and their Cecal tonsil were taken out and prepared for EM (Electronic Microscope) assay and light microscopic study. By light microscopic study about numeration of apoptotic cells, statistic difference were appeared (p = 0.000) between control and experimental groups. With EM, apoptotic cells were appeared by submargination of chromatin of nuclear membrane concurrent chromatin condensation in experimental group but there were not any apoptotic cells in control group. Apoptosis was appeared by attachment of virus to IgM+ receptors of LB surface and to enforce of cells to secretion of some cytokines. VP2 and 17KD were major viral proteins induced apoptosis in bursa and spleen in infected chickens. In this study and previous studies were demonstrated that IBDV (Infectious Bursal Disease Virus) affected chickens with both of necrosis and apoptosis.