Background/Aim: Cervical cancer is considered poorly chemo-sensitive in women and its treatment remains unsatisfactory. Cyperus rotundus is used in Chinese medicine as a therapeutic agent for women's disease. The effects and molecular mechanisms of the ethanol extraction of C. rotundus (CRE) on cervical cancer remain unclear. We aimed to explore the mechanisms and genetic influence of CRE on cervical cancer. Materials and Methods: HeLa, human cervical cancer cells were treated with various doses of CRE and changes in cell morphology and cell viability were assessed using microscopy and flow cytometry. Finally, we performed a microarray analysis to scan related genes. Results: The treatment of CRE on HeLa cells caused morphological changes and induced chromatin condensation. DNA microarray analysis showed that CRE led to up-regulation of 449 genes and downregulation of 484 genes, which were classified in several interaction pathways. Conclusion: CRE changed HeLa cell morphology and induced gene expression which associated with apoptosis and cell-cycle arrest. These results provide important information at the transcription level for targeting treatments of human cervical cancer.Cyperus rotundus L. (Cyperaceae) has been extensively used in traditional medicine in Asia, Africa, and Europe. It is also known as nutgrass and is cultivated widely in tropical, subtropical and temperate regions. It is prescribed for gynecological disorders, including dysmenorrhea and irregular menstruation, while its rhizomes (rootstalks) have been used as sedatives and analgesics (1, 2). Recently, many studies have demonstrated that its rhizomes have a vast range of biological and pharmacological functions, including anti-oxidant, antiinflammatory, anti-diabetic, anti-allergic, anti-nociceptive and anti-cancer effects (2-4). The active chemical constituents of C.