Abstract: The present invention provides a frequency domain near infrared oximeter (fdNIRS) instrument and associated method of determining the oxygenation level of tissue. The tissue is irradiated by a near infrared light source whereby the incident light passing through the tissue is detected by a light detector. Specifically, light signals of a single frequency at at least three separate wavelengths are provided from the near infrared light source. The near infrared light signals are collected with the light detector and, the phase differences between the collected near infrared light signals and a reference near infrared light signal are determined. The fdNIRS oximeter utilizes frequency domain technology to monitor phase shifts relative to a reference signal to derive SO2 through photon transport and Beer-Lambert equations.