Mitochondria are the cellular organs responsible for the cell's energy production. Mitochondria are special in that their DNA, their building plan, is different from the rest of the cell and behaves like the DNA of a bacterium. One cell has many mitochondria and each mitochondrion has many copies of mitochondrial DNA in it. Because mitochondria are passed from mother to child, unlike most of your normal DNA, you only get mitochondrial DNA from your mother's side. Alzheimer's disease and Parkinson's disease are both degenerative diseases of the brain that are affected by many factors. It often takes years for someone to be diagnosed with Alzheimer's or Parkinson's; it is also difficult to predict in whom the diseases will occur. Current treatments can slow down the diseases somewhat, but not cure them. In this study, we look at whether a link can be found between mitochondrial DNA mutations and Alzheimer's and Parkinson's diseases. We confirm that in both Parkinson's and Alzheimer's, mitochondria are affected by the presence of the disease, but that diseased mitochondria themselves can also influence the evolution of the disease. We find three inherited mutations that can affect the risk for the diseases. One of these mutations increases the risk of both Alzheimer's and Parkinson's, a second mutation potentially increases the risk of Alzheimer's and a third potentially decreases the risk of Parkinson's. The location and function of these mutations aligns with an existing theory that the overproduction of a harmful substance called reactive oxygen can damage DNA and the cell. For Alzheimer's, we find insufficient evidence to further explain the mechanism of the disease. For Parkinson's, we do find evidence about the behavior of mitochondria. Reactive oxygen, harmful factors or inadequate repair mechanisms cause DNA copies in the mitochondria to form from which a complete piece is missing. These are called deletions. Too many deletions prevent mitochondria from performing their functions correctly. In normal circumstances, the cell will decide to discard these malfunctioning mitochondria and increase the production of healthy mitochondrial DNA. Parkinson's occurs because in specific cells in the brain, the sick mitochondrial DNA with deletions will continue to multiply.