The temperature of lithium-ion cell and module has a significant impact on performance and ageing. Therefore, it is crucial predicting the temperature distribution and evolution of lithium-ion batteries. However, most of the electrothermal models consider a simplified cell geometry. In this work, a 3D electrothermal model of prismatic cells is developed based on the internal geometry reconstructed from tomography. The numerical results for one single cell and a module of 12 cells in series (12S) are compared to experimental measurements for charge and discharge at different current-rates (C-rates). This study shows a cooling process due to entropy change at low C-rate while at higher C-rate the Joule effect is predominant. The real cell geometry highlights the non-uniform temperature distribution induced by the inert gas and anisotropic thermal conductivity of the jelly roll. Finally, higher internal temperatures are observed in the module because of its architecture.