Background Percutaneous radiofrequency thermocoagulation of the trigeminal ganglion (PRTTG) is regarded as the first choice for most patients with trigeminal neuralgia (TN) because of its safety and feasibility. However,neuronavigator-guided PRTTG has been seldom reported. The purpose of this study was to assess the safety and efficacy of neuronavigator-guided PRTTG for the treatment of intractable TN.Methods Between January 2000 and December 2004, 54 patients with intractable TN were enrolled into this study and were randomly divided into two groups. The patients in navigation group (n=26) underwent PRTTG with frameless neuronavigation, and those in control group (n=28) received PRTTG without neuronavigation.Three months after the operation, the efficacy, side effects, and complications of the surgery were recorded. The patients in the control group were followed up for 10 to 54 months (mean, 34±5), and those in the navigation group were followed up for 13 to 58 months (mean, 36±7). Kaplan-Meier analyses of the pain-free survival curves were used for the censored survival data, and the log-rank test was used to compare survival curves of the two groups.Results The immediate complete pain-relief rate of the navigation group was 100%, whereas it was 95% in the control. The proportion of sustained pain-relief rates at 12, 24 and 36 months after the procedure were 85%, 77%,and 62% in the navigation group, and 54%, 40%, and 35% in the control. Recurrences in the control group were more common than that in the navigation group. Annual recurrence rate in the first and second years were 15% and 23% in the navigation group, and 46%, 60% in the control group. No side-effect and complication was noted in the navigation group except minimal facial hypesthesia.Conclusion Neuronavigator-guided PRTTG is a safe and promising method for treatment of intractable TN with better short- and long-term outcomes and lower complication rate than PRTTG without neuronavigation.