NIRS (Near-infrared Spectroscopy) and DOI (Diffuse Optical Imaging) are relatively new, non-invasive, and non-ionizing methods that measure or image optical properties (Scattering and Absorption Coefficient) and physiological properties (Water Fraction, concentration of Oxy-, Deoxy-Hemoglobin, Cytochrome Oxidase, etc) of biological tissues. In this paper, three different types of NIRS systems, mathematical modeling, and reconstruction algorithms are described. Also, recent applications such as functional brain imaging, optical mammography, NIRS based BMI (Brain-Machine Interface), and small animal study are reviewed.