In this study, the purpose was to investigate the histopathological, genotoxic effect, oxidative stress and cell death due to Metronidazole (MTZ), which is a 5-nitroimidazole compound used widely for the treatment of anaerobic organism infections in fish and humans on gill and liver tissues of Oncorhynchus mykiss.Trout fishes were exposed to 5, 10, and 20 mg/L of MTZ in the aquariums for 2, 4 and 8 days. Staining technics namely H&E, NOS immunohistochemistry, and TUNEL were performed to determine histopathological changes, oxidative damage and apoptosis. Additionally, smear preparations were also prepared from gill blood for genotoxic evaluations. The organ damage started in the 2nd day with 5 mg/L MTZ application and effects increased per duration and dose-dependent manner. It was observed that the gills had the primary and secondary lamellae lengths, with formation of clavate lamellae, fusion in secondary lamellae, separation of epithelium and aneurysm. Regional necrosis, vacuolization of hepatocytes, pycnotic nucleus, enlarged sinusoids were also determined in the liver. NOS immunoreactivity increased with the inducible immunoreactivity (iNOS) that was more prominent when compared to the endothelial immunoreactivity (eNOS). Apoptotic immunoreactivity was higher in the 10 mg 8th day experimental group at liver and gills, and was lower 20 mg 8th day experimental group. When the gills and liver compared with each other, in all doses, immunoreactivity was lower in gills, compared with liver. Genotoxic examinations showed that both number of micronucleated erythrocytes and nuclei abnormalities were higher in MTZ-treated groups.