DNA methylation is an epigenetic modification associated with gene transcription regulation, X-chromosome inactivation, regulation of development and cell differentiation. Aberrant DNA methylation has been linked to cancer. The advent of microarray technology has provided new opportunities for high-throughput study on DNA methylation. Various microarray-based methods depend on different pretreatments including immunoprecipitation and restriction digestion. Al-though each technique has its limitations, the immunoprecipitation method has high specificity, and the restriction digestion method shows high sensitivity. Together they provide many choices to the study of genome-wide DNA methylation profile in cancer.