Mitochondria are among a cell's most vital organelles. They not only produce the majority of the cell's ATP but also play a key role in Ca buffering and apoptotic signaling. While proper allocation of mitochondria is critical to all cells, it is particularly important for the highly polarized neurons. Because mitochondria are mainly synthesized in the soma, they must be transported long distances to be distributed to the far-flung reaches of the neuron-up to 1 m in the case of some human motor neurons. Furthermore, damaged mitochondria can be detrimental to neuronal health, causing oxidative stress and even cell death, therefore the retrograde transport of damaged mitochondria back to the soma for proper disposal, as well as the anterograde transport of fresh mitochondria from the soma to repair damage, are equally critical. Intriguingly, errors in mitochondrial transport have been increasingly implicated in neurological disorders. Here, we describe how to investigate mitochondrial transport in three complementary neuronal systems: cultured induced pluripotent stem cell-derived neurons, cultured rat hippocampal and cortical neurons, and larval neurons in vivo. These models allow us to uncover the molecular and cellular mechanisms underlying transport issues that may occur under physiological or pathological conditions.