Transition metal oxides are a class of materials that are vitally important for developing new materials with functionality and smartness. The unique properties of these materials are related to the presence of elements with mixed valences of transition elements. Electron energy-loss spectroscopy (EELS) in the transmission electron microscope is a powerful technique for measuring the valences of some transition metal elements of practical importance. This paper reports our current progress in applying EELS for quantitative determination of Mn and Co valences in magnetic oxides, including valence state transition, quantification of oxygen vacancies, refinement of crystal structures, and identification of the structure of nanoparticles.