The effects of acupuncture have been described and handed down empirically for centuries but there are few reports based on objective data. The aim of this study was to provide selective evidence of a specific effect of acupuncture on the brain and the eye using a Doppler ultrasound technique. A transcranial Doppler sonography arrangement was developed to monitor blood flow profiles in the supratrochlear and middle cerebral arteries simultaneously and continuously. Two acupuncture schemas were tested in a randomized cross-over study with 13 patients with ophthalmologic diseases. Applying acupuncture needles to special eye points increased the blood flow velocity in the supratrochlear artery significantly (p < 0.001) compared to the reference interval before acupuncture. In the middle cerebral artery only a minimal, non-significant increase in blood flow velocity was seen. In contrast, acupuncture of points that are held to increase cerebral blood flow velocity increased blood flow velocity in the middle cerebral artery significantly (p < 0.001) while leaving that in the supratrochlear artery unchanged. Specific acupuncture produce specific, reproducible quantifiable effects on blood flow velocity in arteries to the brain and eye.