In this study we examine and describe the changes in the hemoglobin oxygenation and the Cytochrome-C-Oxidase redox state that are caused by the pulsatile character of the blood flow in the human head. We used near-infrared spectroscopy (NIRS) in combination with simultaneously recorded ECG and Transcranial Doppler sonography of arteries and veins and show that there is a distinct time lag between heart activity, arterial blood flow, hemoglobin concentration as measured by NIRS and venous blood flow. NIRS has intensively been used to measure functional activation of the brain. When measuring cortical activation by functional stimulation, the pulse signal interferes with the acquired activation signal. We demonstrate that a filter algorithm can remove the pulse artifact and therefore improves the data acquired during visual stimulation.