DNA methylation is an important enzymatic covalent modification of DNA that plays an important role in genome regulation. DNA methylation patterns are fashioned during development and could be altered in response to experience and exposure. Aberrations in DNA methylation patterns are noted in cancer and other diseases. It is therefore extremely important to accurately quantify DNA methylation states for studying physiology and disease as well as for using DNA methylation markers in diagnosis. Here, we review the most commonly used methods for quantifying DNA methylation states of single genes: Pyrosequencing, Quantitative Methylated DNA Immunoprecipitation (qMeDIP), and methylation-sensitive high resolution melting (MS-HRM). Each method is described and required steps are detailed. We also discuss the advantages and disadvantages of the different methods.