The use of a combination of ketamine and xylazine is broadly used either for anesthesia or euthanasia in rodent animal models in research. However, the genotoxicity and mutagenic effects of these drugs are unknown. Therefore, the aim of this study was to evaluate these effects to help the understanding of elevated values in negative controls in genotoxic/mutagenic assays. Sixty CF-1 mice were divided into ten groups of six mice per group: negative control (saline), positive control (doxorubicin, 40mg/kg), ketamine at 80mg/kg and xylazine at 10mg/kg, ketamine at 100mg/kg and xylazine at 10mg/kg, ketamine at 140mg/kg and xylazine at 8mg/kg, ketamine at 80mg/kg, ketamine at 100mg/kg, ketamine at 140mg/kg, xylazine at 8mg/kg, and xylazine at 10mg/kg. After drug induction, the blood cells were analyzed at 1, 12, and 24h by the comet assay, while the brain cortex, liver, and kidney cells were verified just at 24h by the comet assay and bone marrow was tested at 24h by micronucleus test. The positive control was significantly different in relation to the negative control in all times and tissue analyzed. The dose of ketamine at 140mg/kg plus xylazine at 8mg/kg and only ketamine at 140mg/kg exhibited a genotoxic effect in blood and brain cells at all the times analyzed. The doses of ketamine at 80 and 100mg/kg in association or not with xylazine showed increased DNA damage at 1 and 12h, but this effect was reversed after 24h of drug administration. The liver, kidney, and bone marrow cells of animals treated with ketamine or xylazine isolated or combined did not differ when compared with the negative control. Then, our findings emphasize the necessity of more studies that prove safety of the ketamine use, since that anesthetic can be able to induce false-negative results in genotoxic experimental studies.