Photoperiod is a significant modulator of behavior and physiology for many organisms. In rodents changes in photoperiod are associated with changes in circadian period and photic resetting of circadian pacemakers. Utilizing rhythms of in vivo behavior and in vitro mPer2::luc expression we investigated whether different entrainment photoperiods (16:8 and 8:16 L:D) alter the period or phase relationships between these rhythms and the entraining light cycle in Per2::luc c57Bl/6J mice. We also tested whether mPer2::luc rhythms differed in anterior and posterior SCN slices. Our results demonstrate that photoperiod significantly changes the timing of the mPer2::luc peak relative to the time of light offset and the activity onset in vivo. In both 8:16 and 16:8 L:D the mPer2::luc peak maintained a more stable phase relationship to activity offset, while altering the phase relationship to activity onset. Following the initial cycle in culture, the period, phase and peaks per cycle were not significantly different for anterior vs. posterior SCN slices taken from animals within one photoperiod. Following short photoperiod treatment, anterior SCN slices showed increased amplitude Per2::luc waveforms and posterior SCN slices showed shorter duration peak width. Finally, the SCN tissue in vitro did not demonstrate differences in period attributable to photoperiod pretreatment, indicating that period aftereffects observed in behavioral rhythms following long and short day photoperiods are not sustained in Per2::luc rhythms in vitro. The change in phase relationship to activity onset suggests Per2::luc rhythms in the SCN may track activity offset rather than activity onset. The reduced amplitude rhythms following long photoperiod treatment may represent a loss of coupling of component oscillators.