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Early and accurate diagnosis of cancer plays a very important role in cancer treatment. The DNA methylation of tumor suppressor genes has been used as a diagnostic biomarker of early carcinogenesis. The 5-methylcytosine of CpG islands in the promoter region has been demonstrated as an evidence of DNA methylation. In this study, the entire process for performing DNA methylation assay including capturing of target DNA, HpaII and MspI endonuclease digestion and nucleic acid amplification have been realized in an integrated microfluidic system. The limit of detection in the microfluidic system was experimentally found to be 102 cells/reaction. The entire process from sample loading to results observed only takes 3 hrs. Rapid diagnosis of ovarian cancer cells in the integrated microfluidic system has been demonstrated by using cell lines and clinical samples. The developed micro system may be promising for early diagnosis of cancers.