Daily restricted feeding (RF) can produce food-entrainable oscillations in both intact and suprachiasmatic nucleus (SCN)-lesioned animals. Thus, there are two circadian rhythms, one of which is SCN-dependent and the other SCN-independent. Recently, it has been established that several mouse clock genes, such as mPer1, mPer2 and mPer3 are expressed in the SCN and other brain tissues. Although the role of mPer genes expressed in the SCN has recently been evaluated in the SCN-dependent rhythm, their function in the SCN-independent rhythm is still poorly understood. In order to understand the role of these genes in SCN-independent rhythm, we examined the expression pattern of mPer1 and mPer2 mRNA in each brain area of mice under RF. Mice were allowed access to food for 4 h during either the daytime under a light-dark cycle or the subjective daytime under constant dark. After 6 days of scheduled RF, the night-time or subjective night-time peak of mPer mRNA changed to a daytime peak in the cerebral cortex and hippocampus, with moderate expression in the striatum, pyriform cortex and paraventricular nucleus, and no expression in the SCN. The daytime peak in the cerebral cortex returned to a night-time peak after the release of RF to a free-feeding schedule. Although the basal rhythm of mPer expression disappeared in SCN-lesioned mice, RF produced mPer mRNA rhythm in the cerebral cortex of these mice. The present results provide evidence of an association between food-entrainable oscillations and the expression of mPer1 and mPer2 in the cerebral cortex and hippocampus.