While the consequences of nuclear DNA damage have been well studied in a number of cell types, the exact consequences of acute and targeted mitochondrial DNA damage is less well understood. This dissertation focuses on the examination of the outcomes of DNA damage directed at neuronal mitochondrial DNA in the absence of nuclear DNA damage. I have used a microfluidic chamber model that allows for the spatial and fluidic isolation of neuronal soma (containing the nucleus and mitochondria) from the axons (containing mitochondria). I found that exposure of the DNA-damaging drug cisplatin selectively to the axons was capable of inducing mtDNA damage in the axonal mitochondria without nuclear damage,. Exposure of neuronal axons and mitochondria to the DNA damaging drugs cisplatin, d4T, or camptothecin all resulted in the degeneration of the exposed axons. As there are three well-recognized pathways which are known to regulate axon degeneration in neurons, I investigated their roles in cisplatin-induced axon degeneration. First, I found that deficiency of the proteins Bax and Caspase was unable to save neuronal axons from degeneration. Additionally, inhibition of caspase activity using a pan-caspase inhibitor also was unable to prevent axon degeneration. These findings indicate that the axon degeneration induced by cisplatin exposure is not mediated by the apoptosis degenerative pathway or the axon pruning pathway. I found that deficiency of Sarm1, an essential component of the Wallerian axon degeneration pathway, was also unable to save against this degeneration. However, addition of the antioxidant glutathione was capable of inhibiting cisplatin-induced axon degeneration. Thus, we find that the axon degeneration induced by cisplatin damage to mtDNA does not appear to be mediated by any of the known pathways of axon degeneration. I also found that cisplatin exposure to axonal mitochondria led to a number of deficits in mitochondrial function—including mitochondrial aggregation, loss of mitochondrial membrane potential, production of reactive oxygen species, and inhibition of mitochondrial trafficking. These findings indicated that directed mtDNA damage, in the absences of nuclear DNA damage, is capable of inducing significant mitochondrial deficits and eventually inducing cellular degenerations.