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Background and Objectives: Malachite green (MG) is a triarylaminmethane dye used in the fish industry as an anti-fungal agent. Concern over MG is due to the potential for consumer exposure, suggestive evidence of tumor promotion in rodent liver, and suspicion of carcinogenicity based on structure-activity relationships. In order to evaluate the risks associated with exposure to MG, we examined the mutagenicity and biochemical effect of MG., Materials and Methods: For genotoxic effect we use the doses 27, 91, 272 and 543 mg/kg b.wt. for different period of time (7, 14, 21 and 28 days) to evaluate chromosomal aberrations in mouse somatic and germ cells as well as sister chromatid exchanges in bone marrow cells. For DNA fragmentation assay from mouse liver the same doses of MG were used for 28 days. For measuring biochemical parameters such as glycolysis and gluconeogenesis enzyme pathways, antioxidant indices, hepatic marker enzymes, total protein, glucose, glycogen levels and liver function enzyme activities were evaluated. Mice were treated orally up to 28 days with the two high doses of MG 272 and 543 mg/kg b.wt., Results and Conclusions: Our results show that MG induce elevation in the percentage of SCE's and chromosomal aberrations (p < 0.01) after treatment with the high doses for long period of time. MG also induces DNA damage in mice liver in a dose dependent manner. Beside, MG treatment either in low or high doses causes biochemical disturbances in the major glucolytic-gluconeogenic pathways, hepatic marker enzymes, depleted glutathione and increased free radical as determined by increasing lipid peroxide. Histopathological observations revealed that MG induced sinusoidal, congestion, focal necrosis and degenerating in hepatic cells, hypertrophy and vacuolization followed by necrosis and cirrhosis.