Fast confocal spectral imagers are provided. A fast confocal spectral imager according to the invention includes a spectral imager coupled to a fast confocal microscope. A laser is provided for generating laser light, which passes through scanning optics which are configured to scan a line- or slit-shaped region of a specimen at a given time. The light then passes through an objective lens and excites fluorescent dyes applied to the specimen, causing the dyes to fluoresce at respective emission spectra. The fluorescence radiated by the excited dyes then passes back through the scanning optics and is directed to a fixed slit that functions as an entrance slit for a spectral imager. The spectral imager receives the fluorescence and separates it into wavelength bands. The wavelength and position across the slit-shaped region of the specimen for each wavelength band are then recorded.