A novel Monte Carlo (MC) technique for photon migration through 3D media with the spatially varying optical properties is presented. The employed MC technique combines the statistical weighting variance reduction and real photon paths tracing schemes. The overview of the results of applications of the developed MC technique in optical/near-infrared reflectance spectroscopy, confocal microscopy, fluorescence spectroscopy, OCT, Diffusing Wave Spectroscopy (DWS) and Doppler flowmetry are presented.