Mammalian hibernation is characterized by prolonged dormancy consisting of pronounced depression of metabolism and body temperature. Though hibernation occurs in at least seven mammalian orders and several families of the order Rodentia, the ecology and physiology of hibernation in rodents has been most extensively studied in the family Sciuridae, particularly in the so-called ground squirrels, that is, the tribe Marmotini. Early studies of these rodents demonstrated the important role of an endogenous circannual clock in the persistence of annual timing and phasing of key seasonal events, including weight gain, hibernation and reproduction. Here, we review the causes and consequences of intraspecific variation in the timing of hibernation and reproduction in these sciurids and examine the physiological mechanisms that contribute to phenotypic plasticity in seasonal timing. Although the duration, annual phasing and predictability of seasonal change in environmental conditions likely promoted the evolution of endogeneity, precision and brevity of breeding seasons in the annual cycles of sciurids, substantial intraspecific variation in hibernation and reproductive phenology exists along latitudinal and altitudinal clines, as well as among locally varying environmental micro-conditions. We suggest that much of this variation is a function of plasticity in the physiological mechanisms controlling annual cycles. While studies of captive animals have been instrumental in establishing the role of an endogenous rhythm, a greater emphasis on experimental field manipulations is needed to better understand the function, causes and consequences of phenological shifts in wild populations. Ultimately, the capacity of hibernators to adjust their timing in response to changing environmental conditions, either through phenotypic plasticity or microevolution, will be an important determinant of the resilience of sciurid species to changing climate.