Objective: To observe the clinical disinfection effect of root canal with non-filling medication. Methods: 36 patients who required root canal therapy(RCT) for apical periodontitis (acute or chronic) or pulp necrosis were involved in the study.RCT was completed after two visits in both groups. Non-filling medication was used as disinfection in 18 teeth of 18 patients (experimental group) while FC in another 18 teeth of 18 patients (control group) randomly at first visit.One week later,root canal was regularly filled to complete RCT.From each case, bacteria specimens were collected and identified before sealing and filling. Results: Bacteria were detected in every specimen in both groups before sealing,which were mixture of aerobes and anaerobes.One week later,only one strain was detected in one specimen of each group. Conclusion: Non-filling medication can be used as an effective disinfection to sterilize root canal.