DNA methylation is likely to regulate the expression of clock genes during normal development and in the development of cancer. Methylation status of clock genes also appears to be associated with dementia with Lewy bodies and aging. However, there is currently no rapid, cost-effective method to examine the methylation status of clock promoters in mice. In the present study, two sets of methylation-specific polymerase chain reaction assays were developed to examine the methylation status of eight key clock genes, Bmal1, Bmal2, Clock, NPAS2, Per1, Per2, Cry1 and Cry2. Down to 1% of methylation can be examined consistently with this method, demonstrating high specificity and sensitivity. The methylation of clock promoters was examined in five peripheral tissues with the developed method; indicating that all of the clock promoters are free from methylation in the adult mouse.