Mitochondria are highly dynamic organelles, whose morphology can vary from an elongated and interconnected network to fragmented units. In recent years, outstanding discoveries have linked mitochondrial morphology to the regulation of an increasing number of biological processes, such as biosynthetic pathways, oxidative phosphorylation and ATP production, calcium buffering, and cell death. Here we describe two of the main methods used to analyze the mitochondrial length in fixed cells and the mitochondrial fusion rate in live cells. Moreover, we focus one of the protocols on T cells, as an example of non-adherent cells, which present some particularities and difficulties in the analysis of mitochondrial shape. We also discuss the main mouse models carrying a mitochondrial targeted fluorescent protein, an invaluable tool to deeply investigate in vivo mitochondrial morphology.