BACKGROUND Transcranial Doppler sonography (TCD) has been used widely for long-term monitoring of cerebral blood flow without adverse reports. However, attention has not been adequately paid to the fact that an increase in the time period of TCD insonation causes brain temperature to rise due to ultrasound absorption by tissue and the skull. We measured the actual temperature rise in local brain tissue induced by TCD insonation over a long time period during in vivo animal experiments in order to verify whether or not a pause is required in long-term, continuous TCD monitoring. METHODS We inserted thermocouples into the skull-brain interface (SBI) of 15 New Zealand White rabbits (10: TCD application group; 5: control group, TCD non-application group). The TCD probe was placed on the parietal bone, and changes in SBI temperature (SBIT) were measured for 90 min. TCD was set at maximum output level (0.2 W, 2 MHz). RESULTS SBIT in the TCD group increased rapidly to 3.47 degrees C within 25 min and then reached a plateau. The maximum time for safe continuous TCD application is estimated to be 33 min. CONCLUSIONS Even though there are large differences in factors, such as brain volume and environmental conditions, between rabbits and humans, there is less difference in their cerebral blood flow per brain weight, which is the parameter that is mainly associated with heat reduction. Accordingly, the findings of the present experiment suggest that long-term TCD monitoring in clinical use should include a pause after every 30 min of insonation to avoid thermal damage to the brain surface.