Plants react to a virus infection at the molecular levels. These reactions are often accompanied by pathological changes on the cellular level and eventually become macroscopically visible as symptoms. Investigation of these modifications demonstrates the host biochemical responses. With the knowledge of these responses we are able to alleviate the pathogenicity of a pathogen with interfering in the different course of infection. This investigation was performed to study the cytological effect of Potato virus Y on tobacco plants (Nicotiana tabacum cv White Burley) chosen as a model plant. For this aim, leaf extract of infectious potato plants were mechanically inoculated to tobacco plants. Two weeks after inoculation and simultaneous with the systemic symptoms appearance, samples of mottel chlorotic areas (2-4 mm2) prepared and were fixed in glutaraldehyde, post fixation was accomplished by treatment with osmium tetroxide. After dehydration the specimens were embedded in spur medium, specimens were cut on ultra microtome. Sections were observed with light and electron microscope after staining with uranyl acetate and lead citrate. After viewing the specimens results were as follows: degenerated cytoplasms, nucleus was enlarged and became lobed, number and the size of mitochondria were increased, number and the size of chloroplasts were decreased and arrangement of thylakoides were messed, malformation and swelling the membrane of chloroplasts were also observed and increase in the proteinaceous chloroplast pigments (plastoglobuli) became obvious. Number of paramural bodies increased and we observed most often viral inclusion bodies along with the endoplasmic reticulum due to systemic infection. According to the results we conclude that respiration of infected cells increased and photosynthesis decreased and also metabolism system of host was become too activated due to the viral infection. Results indicate the hypersensitive response like mechanism involve in the systemic infection of potato virus Y.