AimCyclophosphamide is an effective anti-tumor agent, however, it induces genomic instability and tissue toxicity in clinical application. This study aims to evaluate the action of piperlongumine against cyclophosphamide-induced toxicity. Main methodsThe action was investigated in rodent model of genomic instability, where piperlongumine (50 mg/kg) was orally co-administered with cyclophosphamide (5 mg/kg) for 28 days to Wistar albino rats. Further, piperlongumine was also examined for acute and sub-acute toxicity. Key findingsPiperlongumine significantly reversed genotoxicity in high-proliferation tissue (bone marrow: p < 0.05) as well as in vital tissues (hippocampus: p < 0.01 and hepatocytes: p < 0.05), calculated as micronuclei formation and %DNA fragmentation. It also restored the redox homeostasis, counteracted the formation of oxidative DNA damage product and DNA double-strand break in vital tissues, indicated by reduction of 8-OHdG and γH2AX. TUNEL assay revealed that piperlongumine diminished the cyclophosphamide-associated apoptotic cell death in hippocampus as well as in liver tissue and conferred cytoprotection to the host. These findings were finally corroborated with the histopathological findings, where piperlongumine treatment restored the cellular viability of liver and hippocampus. Further, piperlongumine did not produce any toxic effects to rats in systemic toxicity studies. SignificancePiperlongumine possesses genome stabilizing effect and reduces cyclophosphamide-associated DNA damage, oxidative stress, hepato-, and neurotoxicity, diminishes the DNA damage response pathway in the rat model, at the same time, conserves the micro-architectural details of liver and hippocampus. The findings are significant in terms of reducing genotoxic impact of chemotherapy-receiving patients.