Epigenetic marks of DNA such as 5-methylcytosine control the levels of gene expression in cells and tissues by altering DNA structure, inhibiting transcription factor binding, and recruiting chromatin-modifying enzymes. DNA methylation marks are introduced in both strands of DNA by DNA methyltransferases, allowing for heritable gene silencing. In addition to 5-methylcytosine, cells contain its oxidized forms 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, as well as recently discovered DNA marks, 4-methylcytosine and 6-methyladenosine. Structural identification, quantitation, and mapping of DNA epigenetic marks are critical for our understanding of epigenetic control in healthy cells and to allow for insight into epigenetic deregulation in human disease and the efficacy of epigenetic therapies. This review focuses on experimental techniques and methodologies that can be used to study epigenetic modifications of DNA, including methods for quantifying global levels of epigenetically modified nucleosides and sequencing techniques for mapping the locations of various epigenetic marks along the genome, leading to better understanding of their biological functions and dynamics.