Abstract This paper provides an overview of phonon measurement using electron energy loss spectroscopy (EELS) in the electron microscope, with polar cubic boron nitride (c-BN) and nonpolar diamond crystals as representative examples. Differential scattering cross-sections for phonon creation and annihilation are reviewed, highlighting the influence of crystal polarity under kinematical and dynamical scattering conditions. The temperature dependence of EELS intensity is examined, with local absolute temperature evaluated by analyzing the ratio of phonon annihilation to creation intensities. Practical aspects and challenges associated with phonon measurement in EELS are also discussed, together with future perspectives in this evolving field.