The entropy change (ΔS) of a Li-ion battery during its charging and discharging is one of the important parameters, which has a strong effect on the heat generation in a Li-ion battery during its operation. Moreover, the behavior of the entropy change during an aging of the Li-ion battery may be used for the analysis of the battery degradation, the state of health estimation and prediction. Unfortunately, the determination of the ΔS with a high accuracy is a difficult task. Currently, the potentiometric method for the determination of the ΔS is considered as the most popular method. However, measurements of the ΔS by the potentiometric method takes a lot of time as all measurements should be done in steady-state conditions to obtain acceptable accuracy. ΔS can be also measured by the calorimetric method but this method requires utilization of expensive equipment such as a very accurate calorimeter and, therefore, it is rarely used. A method, recently presented for the ΔS determination by using heat flux measurements on the surface of a cylindrical Li-ion cell, may be considered as a modification of the calorimetric method. According to this method, the ΔS is obtained from the total heat generation during charging and discharging of a Li-ion battery, similarly as it is done in the calorimetric method. However, the heat generation is calculated by using a thermal model of the cell and measured values of the temperature on the cell surface and heat flux from this surface. This method does not require any expensive equipment and the required time of measurements is significantly smaller than in case of the potentiometric method, as steady-state conditions are not required for the determination of ΔS. Unfortunately, the uncertainty of the presented method is still under a question. Therefore, this work is dedicated to the analysis of the effect of different test conditions on the uncertainty of the ΔS measurements when using heat flux and temperature sensors. Energy and power -type cylindrical Li-ion cells are used during the analysis. The two different types of the cylindrical cell are selected with purpose to verify the applicability of the method not only for the power cells, as it was done previously, but also for the energy cells, where the effect of the ΔS on the total heat generation is lower than in power cells. Cylindrical Li-ion cells are used in the research, because the heat generation in them is usually lower than in pouch or prismatic Li-ion cells. Therefore, the uncertainty for the heat generation measurements in cylindrical cells should be higher than in pouch and prismatic cells. The entropy changes in both selected Li-ion cells are measured by the potentiometric method for different values of the state of charge (SoC) and these curves are used as a reference for the analysis of the effect of the test conditions. The heat generation in the considered Li-ion cells is measured with the help of a thermal model of the cylindrical cell and measured values of the temperature and the heat flux flowing out from the cell surface during its charging and discharging. The effect of the ambient temperature and current C-rate on the uncertainty of the ΔS determination is presented by considering different ambient temperatures and current C-rates during the heat measurements and following the calculation of the ΔS and its uncertainty.