Thermal runaway is a major cause of failure in Li-ion batteries (LIBs), and of particular concern for high energy density transport applications, where safety concerns have hampered commercialisation. A clear understanding of electro-thermal properties and how these relate to structure and operation is vital to improving thermal management of LIBs. Here a combined thermal imaging, X-ray tomography and electrochemical impedance spectroscopy (EIS) approach was applied to commercially available 18650 cells to study their thermal characteristics. Thermal imaging was used to characterise heterogeneous temperature distributions during discharge above 0.75C; the complementary information provided by 3D X-ray tomography was utilised to evaluate the internal structure of the battery and identify the regions causing heating, specifically the components of the battery cap.