Circadian rhythms in locomotor activity in nocturnal animals typically show activity during the night followed by quiescence during the day. In hamsters, this activity pattern can be altered by confining them to novel running wheels for a few hours during the day, thereby inducing them to be active. After several days of induced activity, two bouts of activity occur spontaneously, one during the day, and the other at night. This phenomenon is known as behavioral decoupling. In the present study we examined the effects of behavioral decoupling on the pattern of SCN Per expression. Our results show robust expression of Period genes in the SCN of animals killed during either of the two inactive phases within a 24-h period, and weak expression of those genes in the SCN of animals killed during the two active phases. This contrasts with the circadian rhythm of Per expression typically seen in the SCN of entrained or free running animals. Our data support the idea that behavioral decoupling reorganizes the circadian system in a manner different from that produced by constant light-induced splitting and constant dark splitting.