Colorectal cancer (CRC) is one of the most common cancers worldwide. CRC develops from precancerous polyps in the colon or rectum and is preventable by an early diagnosis and with the removal of precursor lesions. Numerous genetics and epigenetic alterations transform benign polyps to malignant tumors by affecting different pathways. Over the past decade, increasing evidence represent the utility of cell-free DNA as a ‘liquid biopsy’ to supplement non-invasive biopsies for genetic and epigenetic characterization and monitoring of solid cancers. One of the epigenetic biomarkers that has gained more attention in CRC is aberrant DNA methylation of Septin 9 gene. In this study we try to evaluate the methylation of Septin 9 gene status in the cfDNA of the plasma in colorectal cancer patients. Plasma cell-free DNA samples were extracted from 30 patients with background of tumors or polyps and 30 samples from healthy individuals. Septin 9 methylation analysis was performed by using the bisulfite specific high resolution melting analysis. The result showed a sensitivity and specificity of 10% and 53.33%, respectively. In conclusion, our results demonstrated that Septin 9 DNA methylation in plasma determined by THP and BSP-HRM had not have sufficient accuracy.