A simplified in vivo near infrared spectroscopy (NIRS) system for functional brain analysis and a protocol for the study of visual evoked potentials in the human brain is presented. A novel NIRS system bases on a simple photon counting technique using a CW light source (laser diode at 780 nm), fibre optodes delivering light to the subject and from the subject to detector, a photomultiplier tube (PMT) for high infra-red (IR) response and the 800 MHz Gated Photon Counter/multichannel scaler (MCS) for data acquisition. A chequerboard stimulus was used to elicit a response signal from the visual cortex. This photon signal arising from the cortical systems of the brain was processed to detect features indicative of the neural processing systems involved.