A new method for the calculation of a stratification efficiency of thermal energy storages based on the second law of thermodynamics is presented. The biasing influence of heat losses is studied theoretically and experimentally. Theoretically, it does not make a difference if the stratification efficiency is calculated based on entropy balances or based on exergy balances. In practice, however, exergy balances are less affected by measurement uncertainties, whereas entropy balances can not be recommended if measurement uncertainties are not corrected in a way that the energy balance of the storage process is in agreement with the first law of thermodynamics. A comparison of the stratification efficiencies obtained from experimental results of charging, standby, and discharging processes gives meaningful insights into the different mixing behaviors of a storage tank that is charged and discharged directly, and a tank-in-tank system whose outer tank is charged and the inner tank is discharged thereafter. The new method has a great potential for the comparison of the stratification efficiencies of thermal energy storages and storage components such as stratifying devices.