Inbred mice have been routinely used in studies of genetic effects that determine behavioral variation due to circadian rhythm. In addition to activity patterns (ACT), the present study aims to characterize variation in the circadian rhythm of deep-body temperature (T_db) and heart rate (HR) in a specific genetic model of differential cardiorespiratory control. Radiotelemeters were implanted in C3H/HeJ (C3, n = 11) and C57BL/6J (B6, n = 11) inbred strains. Reciprocal first-generation offspring, B6C3F1/J (B6F1, n = 8) and C3B6F1 (C3F1, n = 3) mice, were included to initiate an evaluation of heritable phenotypes. The animals were housed individually in a facility maintained at 23-24°C, and the light/dark cycle was set at 12-h intervals. In each animal, repeated measurements were obtained at 30-min intervals, and the circadian patterns of ACT, T_db, and HR were assessed by novel statistical methods that detailed the periodic function for each strain. During the dark-phase, B6 mice demonstrated two distinct peaks in ACT and T_db relative to a single early peak for C3 mice. In contrast to the parental strains, both B6F1 and C3F1 mice demonstrated intermediate second peaks in ACT and T_db. With respect to HR, the C3 strain demonstrated a significantly (P < 0.01) greater daily average compared with B6 mice. In addition, the circadian rhythm in HR differed significantly from the ACT and T_db patterns in B6 mice (but not in C3 mice); that is, the periodicity in HR for B6 mice preceded the rise and fall in ACT and T_db during both peaks. The B6 phenotype was also observed in F1 mice. In conclusion, these data suggest that the circadian regulation of ACT, T_db and HR vary significantly among C3, B6 and F1 mice. Furthermore, phenotypic differences between C3 and B6 strains can be used to explore the genetic basis for differential circadian regulation of body temperature and heart rate.