Transcranial Doppler (TCD) examinations are increasingly being used in studies of headache pathophysiology. Because blood velocity is highly dependent on PCO2, these parameters should be measured simultaneously. The most common way of performing measurements during TCD examinations is as end-tidal pCO2 with a capnograph. When patients are nauseated and vomit, as in migraine, the mask or mouthpiece connected to the capnograph represents a problem. We therefore evaluated whether a transcutaneous pCO2 electrode was as useful as the capnograph for pCO2 measurements in TCD examinations. We conclude that this is not the case, and recommend capnographic end-tidal pCO2 measurements during TCD examinations. However, transcutaneous pCO2 measurements may represent a supplement to spot measurements of end-tidal pCO2 in stable conditions when long-term monitoring is needed, and the mask or mouthpiece of the capnograph has to be taken on and off between recordings.