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Theoretical aspects of methods for calibrating Stokes polarimeters are considered. The prospects and opportunities for implementing the presented methods for calibrating portable polarization systems used in biology and medicine are determined. Based on a comparative analysis, a method for calibrating a portable Stokes polarimeter for medical applications is proposed. The chosen method provides the smallest error in measuring the parameters of the Stokes vector for calculating the parameters of optical anisotropy and researching the polarization properties of biological tissues. A series of experimental research and statistical analysis of the spatial distributions of the polarization parameters of the calibration sample was carried out to use the results for forming the instrument matrix of the developed Stokes polarimeter during calibration.