In this work, we propose the use of Transcranial Doppler Monitoring (TCD) as a tool to measure brain activity during the exposure to Virtual Environments (VE) used in clinical therapy sessions. The technique is non-invasive, and can be easily integrated with Virtual Reality (VR) settings. Moreover, it provides a high temporal resolution, which grants the possibility to analyze changes in brain activity during the evolution of a clinical session and to correlate them with specific events that may occur in the VE. We have performed two studies combining TCD with VR. Results of these studies show that it is feasible to use this technique in combination with VR settings designed for virtual therapy. It was observed that immersion and navigation modifications in the VE generated changes in brain activity that can be detected using TCD.