Disclosed are methods and devices for confocal microscopy in the near-infrared. wavelength. The device uses a near-infrared (NIR) light producing source such as laser; optical components designed to reflect and transmit NIR from a sample; and an NIR detector coupled to a computer for constructing a focal plane image from a raster scan. The detector may be a photodiode or photo-multiplier tube for detecting fluorescence signals in the NIR (800-1700 nm) wavelength range using a variety of NIR-I (800-1000 nm) and NIR-II (1000-1700 nm) dyes and nanomaterials. An imaging method is described using the NIR-confocal microscope for slice by slice 3D imaging of biological tissues throughout a thickness up to, for example, 5 mm in the NIR-II window. The reduced scattering in NIR-II allows for tissue penetration up to about 5-10 mm, superior to ˜0.2 mm afforded by conventional imaging.