The cycle length or period of the free-running rhythm is a key characteristic of circadian rhythms. In this study we verify prior reports that locomotor activity patterns and running wheel access can alter circadian period, and we report that these treatments also increase variability of circadian period between animals. We demonstrate that the loss of a neurochemical, neuropeptide Y (NPY), abolishes these influences and reduces the inter-individual variability in clock period. These behavioral and environmental influences, from daily distribution of peak locomotor activity and from access to a running wheel, both act to push the mean circadian period to a value less than 24 hours. Magnitude of light-induced resetting is altered as well. When photoperiod was abruptly changed from LD18:6 to LD6:18, mice deficient in NPY were slower to respond to the change in photoperiod by redistribution of their activity within the prolonged dark, and eventually adopted a delayed phase angle of entrainment as compared to controls. These results support the hypothesis that non-photic influences on circadian period serve a useful function when animals must respond to abruptly changing photoperiods, and point to the NPYergic pathway from the intergeniculate leaflet innervating the suprachiasmatic nucleus, as a circuit mediating these effects.