Of late, with the emergence of new optical devices and technological advances in data processing, polarization techniques are being increasingly used in biomedicine. Mueller matrix calculus is suitable for describing the polarization properties of biomedical specimens because of its mathematical completeness and compatibility with common optical equipment. Compared with traditional non-polarization optical methods, Mueller matrix polarimetry is sensitive to the scattering induced by subwavelength structures and can provide more information about anisotropic optical properties, including the birefringence and diattenuation of a sample. In this review, we introduce Mueller matrix calculus and related technologies that have great application potential in biomedical studies, including the Mueller matrix decomposition and transformation methods, transmission Mueller matrix microscopes, backscattering Mueller matrix imaging equipment, Mueller matrix endoscopes, and polarization staining techniques. Further, we summarize the improvements in clinical diagnosis made using Mueller matrix polarimetry, such as detection of liver cancer, gastrointestinal cancer, and breast ductal carcinoma tissues. As a label-free, noninvasive, quantitative, and rapid imaging method, Mueller matrix polarimetry has broad application prospects in biomedical studies and clinical diagnosis.