Objective?To investigate the values in clinical application of plasma methylated?Septin9?test in gastrointestinal diseases.?Methods?The data were collected retrospectively from the First Affiliated Hospital of Fujian Medical University from May 2017 to November 2020. A total of 2 128 recipients, including the patients with colorectal cancer (CRC), gastric cancer (GC) and benign digestive diseases, as well as the recipients who were no evidences of diseases (NED), received plasma methylated?Septin9?test (PCR-fluorescent probe method). The relevant clinical data were collected and ROC curve analysis was performed.?Results?The positive rates of plasma methylated?Septin9?test in the pre-operative patients with CRC, GC and benign digestive diseases as well as the NED recipients were 57.67%, 43.71%, 17.72% and 4.88%, respectively. Compared with NED recipients, the sensitivity of plasma methylated?Septin9?test in pre-operative patients with CRC and GC were 57.71% and 43.71%, while the specificity were 95.12% and 95.12%. Furthermore, the positive rates methylated?Septin9?test were increased in the CRC patients (68.92%) and GC patients (48.80%) with TNM stage Ⅲ and Ⅳ, which were more than those in the CRC patients (50.51%) and GC patients (18.82%) with TNM stage Ⅰ and Ⅱ. Similarly, the positive rates in the CRC patients (57.76%) and GC patients (43.71%) before surgery were significantly higher than those in the CRC patients (31.45%) and GC patients (33.76%) after surgery, respectively. After surgery, the results of plasma methylated?Septin9?tests changed from positive to negative in 63.33% CRC patients and 69.23% GC patients. ROC curve analysis demonstrated that the area under the curves (AUCROC) of plasma methylated?Septin9?test between CRC patients and the benign colorectal disease patients or NED recipients were 0.681 or 0.764, while the AUCROC?between GC patients and with gastric disease patients or NED recipients were 0.649 and 0.694 respectively. The combined detections of methylated?Septin9?and carcinoembryonic antigen increased AUCROC?to 0.789 in the patients with CRC and benign colorectal diseases group.?Conclusion?Plasma methylated?Septin9?test have diagnostic values for CRC and GC. However, additional diagnostic methods should still be required.