DNA methylation plays an important role in the regulation of the expression of clock genes during normal development and in the development of cancer. The methylation status of clock genes may also be associated with aging. However, it is unknown whether promoter methylation is also a regulator for the age-related change of clock expression in human total lymphocytes. In the present study, methylation-specific polymerase chain reaction assays were used to examine the methylation status of seven key clock promoters, namely Bmal1, Clock, Npas2, Per1, Per2, Cry1 and Cry2. The methylation status was examined in 298 healthy subjects categorised into three groups according to their age. Noticeable methylation was only detected in the Cry1 and Npas2 promoters, suggesting their epigenetic regulation may be involved in modulating the expression of clock genes and circadian rhythms in leukocytes. However, their methylation frequency did not differ with age or gender.