Exposure of aquatic organisms to organophosphorus pollutants is a subject of keen interest to biologists and environmental scientists. Examining histopathological changes in the tissues of exposed animals can provide great insights to understand the health condition of the organisms. This study examined the effects of malathion concentration and exposure time on the liver and gill tissues of the rainbow trout (Oncorhynchus mykiss) in a laboratory condition and tried to provide a quantitative assessment for the analysis of these effects. The experiment was conducted in three treatments including 0.025, 0.05, and 0.075 mg/L of malathion for 1, 5, and 9 days with a nonexposed group as control, in three replicates. The liver and gill samples were fixed in buffered formalin. About 5 µ tissue sections were prepared using the conventional histological methods and stained using the hematoxylin–eosin method. Histopathological changes in the liver and gill tissues were quantified by grading and the resulting data were analyzed by rank-based estimation. The results showed that histopathological changes in the liver and gill tissues are more affected by the malathion concentration than by the duration of the exposure. However, longer exposure had an intensifying effect on the tissue damage caused by the malathion at higher concentrations. The presence of melanomacrophages as an indicator of malathion toxicity was determined. The fish exposed to 0.075 mg/L malathion for 9 days showed atrophy in the liver and gill tissues, indicating cell death and functional inactivation. Histopathological changes in the liver and gills confirmed the dose-dependent effect of malathion on the rainbow trout.