OBJECTIVE To study the deactivation of the endotoxin in artificial glass root canals with ultrasonic vibration. METHODS 80 artificial glass root canals were randomly divided into 8 groups: Ultrasonic vibration of 5 minutes, 7 minutes, 10 minutes, ultrasonic vibration of 5 minutes together with 3% H2O2 solution, only 3% H2O2 solution, ultrasonic vibration of 5 minutes together with 5.25% NaClO solution, only 5.25% NaClO solution and the control. Standard endotoxin solution was introduced into each root canal. Different time's ultrasonic vibration was applied to different groups. After ultrasonic vibration, the endotoxin activity of each group was tested by kinetic turbidimetric limulus test. RESULTS There were no significant differences among the groups of different time ultrasonic vibration and the control (P>0.05). There was great statistical difference between each group with root canal rinse solution and the control (P<0.001). The endotoxin activity of the test was significantly lower than the control. There was no significant difference between the groups of only rinse solution and rinse solution together with ultrasonic vibration. CONCLUSIONS Under the condition of this study, the only ultrasonic vibration can not deactivate the endotoxin of infected root canals and can not intensify the effect of root canal rinse solution.