This dissertation is focused on the role of DNA methylation in anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV), an autoimmune condition characterized by vascular inflammation and organ damage. Pharmacologically induced remission is complicated by relapses. Potential triggers of relapse are immunological challenges and environmental insults, both of which are associated with changes in epigenetic silencing modifications. Alterations in histone modifications implicated in gene silencing are associated with aberrant autoantigen expression. In Chapter 1 I establish a link between DNA methylation, a model epigenetic gene silencing modification, and autoantigen gene expression and disease status in AAV, by measuring gene-specific DNA methylation of the autoantigen genes, myeloperoxidase (MPO) and proteinase 3 (PRTN3), in leukocytes of AAV patients followed longitudinally (n=82) and healthy controls (n=32). Patients with active disease demonstrated hypomethylation of MPO and PRTN3 and increased expression of the autoantigens; in remission DNA methylation generally increased. Longitudinal analysis divided AAV patients into two groups based on whether DNA methylation increased or decreased from active disease to remission. In patients with increased DNA methylation, MPO and PRTN3 expression correlated with DNA methylation. Kaplan-Meier estimate of relapse revealed patients who increased DNA methylation at the PRTN3 promoter had a significantly greater probability of a relapse-free period, independent of ANCA serotype. Patients with decreased DNA methylation at the PRTN3 promoter were more likely to relapse with a hazard ratio of 4.55. Changes in the DNA methylation status of the PRTN3 promoter predict likelihood of stable remission and may explain autoantigen gene regulation. Chapter 2 focuses on gene-specific DNA methylation patterns of purified neutrophils and CD14+ monocytes isolated from patients with AAV. I measured DNA methylation at MPO and PRTN3 along with the mRNA expression of those genes and found evidence that DNA methylation in monocytes may be contributing to the altered methylation patterns seen in Chapter 1 from total leukocytes while altered expression of autoantigen genes in neutrophils may, instead, be impacted by histone modifications. Efforts to isolate T cells uncovered a CD3- CD4- fraction of cells in our CD4-enriched isolation from active patients exhibiting high autoantigen gene expression which may further contribute to the disease etiology of AAV.