Neuronal mitochondria are essential organelles to maintain synaptic activity due to the high calcium buffering capacity and ATP production. In neurons, mitochondria transport occurs along the microtubules mediated by motor proteins, kinesins and dynein, to drive mitochondria toward the synapses. Disruption of axonal transport is an early pathogenic event in neurodegenerative disorders and growing evidence supports that it may precede neurodegeneration. Here, we describe a method to label mitochondria with fluorescent proteins to monitor their movement along the axons in hiPSC-derived medium spiny neuron-like cells. We also included a detailed protocol for differentiation of hiPSC that produces electrophysiologically mature GABAergic striatal neurons with low amount of glial population.