Abstract: Using terminal deoxyuridine transferase nickend labeling（TUNEL）and electron microscopy technique, the apoptosis were investigated in ducks inoculated with a highly pathogenic avian influenza virus, A/duck/Guangdong/220/2004(H5N1) by intravenous and ocularnasaloralcloacal routes. The results demonstrated that the virusinduced apoptosis occurred in the pancreas, kidney, liver, heart, lung, intestine, cerebrum, cerebellum, thymus, bursa of Fabricius and spleen, etc. The predominent apoptotic cell types were pancreatic acinar epithelial cells, renal tubular epithelial cells, hepatocytes and intestinal epithelial cells. The minority of neurons, glial cells, cardiac muscle cells, epithelial cells of lung air capillary, lymphocytes in the thymus, bursa of Fabricius and spleen also experienced apoptotic changes.