Circadian rhythms are endogenous 24-h rhythms. The suprachiasmatic nuclei (SCN) of the mammalian hypothalamus serve as the master circadian pacemaker, entraining peripheral organs which also demonstrate circadian rhythms. Entrainment to LD cycles of non-24 h duration (T-cycles) induces aftereffects on period that act to bring the intrinsic period closer to the entraining cycle. Both parametric effects, such as changes in endogenous period, and non-parametric effects of light, such as instantaneous phase shifts, act synergistically to accomplish entrainment of the SCN. It is not yet known if entrainment of peripheral oscillators similarly involves both parametric and non-parametric effects. In this study, mPer2(Luc) knockin mice were entrained to either long or short T-cycles, placed into constant darkness (DD) for 3 days to measure behavioral free-running period (FRP), and then PER2::LUC bioluminescence from SCN, spleen, esophagus, lung and thymus was measured in vitro. The FRP of SCN samples was negatively correlated with the FRP of behavioral rhythms, replicating prior results in mPer1-Luc mice. The FRP of the four peripheral oscillators tested did not correlate with behavioral rhythm FRP. Evidence that the SCN may entrain peripheral tissues by shifting phase relationships was observed, in that the phase of PER2::LUC in the SCN relative to peripheral tissues and also to the onset of behavioral activity varied between groups. Our study suggests that aftereffects on FRP may be an emergent property of the system that cannot be explained by the period changes in the system components. Further, we demonstrate that the phase relationship between the rhythm in PER2 in the SCN and these peripheral tissues is altered following T-cycle entrainment.