We analyze temperature dynamics in anatomic pathology samples to identify the most efficient refrigeration method and to predict the time available for optimal sectioning before sample heating, thus getting appropriate information for a correct diagnosis by anatomopathologists. A thermal finite element (FE) analysis was carried out with comsolmultiphysics to evaluate temperature variations in paraffin-embedded tissues, i.e., muscle, bone and fat, and the corresponding thermal stresses. Experiments with different tissues and thermocouple-based measurements allowed validating the FE simulations. Simulations allowed to estimate the time needed to bring the sample at the optimal temperature for sectioning (-8 to -4 °C) in different conditions: refrigeration on a cold plate, refrigeration in a cooled environment, and refrigeration in an environment with forced convection. Among the three cooling methods tested, the forced convection at -20 °C and with an air-flow speed of 5 m/s resulted in the shortest cooling time. As compared to the other methods, thermal stresses can be modulated by varying the air-flow speed. For the different conditions, the time needed for the surface of the tissue block to exit from a temperature corresponding to an optimal cutting, when leaving the sample exposed to room temperature after refrigeration, ranged from 12 to 310 s. We quantify the time needed to adequately refrigerate paraffin-embedded tissue samples and the time available before they leave the optimal temperature window for sectioning. We also evaluate the maximum stress attained in the paraffin block during the cooling and the heating transients. This information will help optimize anatomic pathology processes.