Alzheimer's disease (AD) is a neurodegenerative condition affecting millions of individuals worldwide and is a major source of mortality in elderly populations. While it is well established that there is a strong genetic basis for the disease, the epigenetic mechanism underlying the disease is largely unknown. The main purpose of this thesis is to understand the alteration of epigenetic modifications associated with the disease and its progression. In particular, we examine how alterations in the cytosine methylation and cytosine hydroxymethylation, two epigenetic modifications that are critically important for the development and function of the brain, are associated with advancing stages of Alzheimer's disease. Eight progressive AD brain samples were examined for changes in DNA methylation and hydroxymethylation by both dot blot analysis and a new oxidative bisulfite (OXBS) deep sequencing technology. The initial results of dot blot analysis reveal a statistically significant decrease in 5hmC associated with intermediate stage AD among the samples. This data suggests that the alterations in epigenetic modifications is likely associated with the pathophysiology of Alzheimer's disease, not only shedding new light on our understanding of the epigenetics of the disease, but also providing the basis for our future investigation on the exact cause and effect relationships of these epigenetic changes and their respective stages in Alzheimer's.