Malathion is an organophosphorous insecticide, used in agriculture and a possible source of environmental poisoning. During malathion metabolization, mitochondria generates reactive oxygen species, responsible for significant structural changes. In this study, gills and kidney histological changes in Carassius auratus gibelio exposed to 0.05 mg/l malathion were investigated. In kidney, the effects were dramatic. The 24 -72 hours exposure to malathion induced cytoplasm vacuolization and changes in cell and nuclear volumes. In addition, necrotic renal tubules appeared, nuclear malformations of epithelial cells, anisokary, nuclei pycnosis and nuclei hypertrophy, were noticed. Epithelial ruptures, secondary lamellae fusion and hyperplasia of branchial epithelium, vascular congestion were the main changes noticed soon after pollutant exposure. We suggest that structural changes in gill and kidney could be used as good response to aquatic pollution with organophosphorous insecticides.