Based on the confocal scanning and differential polarization imaging technique, a computer-controlled confocal scanning differential polarization microscope has been built. This system possesses extensive image processing capability that provides digitized regular and/or differential polarization images. This microscope combines the advantages of the confocal design and the extended electronic sensitivity of polarization modulated instrumentation to achieve the measurement of an anisotropy ratio as small as 10-5. In this paper, the basic theory and the instrument are described. In addition, some samples are used to test the actual performance of the system, and it is found that the system provides high resolution (0.3 μm at wavelength 546 nm), reduced depth of field, and high signal-to-noise ratio (83 dB at 10-ms integration time) images. Finally, some biological applications are shown.