A study was conducted to investigate the cardiac autonomic system activity, physical activity, and circadian rhythm of body temperature in children with low waking basal body temperature. Fifty-five boys (aged 9-10 yrs) were evaluated for oral body temperature (OBT) and daily physical activity over a one-week period. Cardiac autonomic nervous system activity was also measured during the same period using a 5-min power spectral analysis of resting heart rate variability. The low temperature group (LOW) was defined as>1 SD below the mean waking OBT (n=6). The 43 individuals with a higher waking OBT score (<1 SD below the mean) served as the control group (C). There were no significant differences in waking time or total sleeping time between LOW and C. However, a low waking OBT, and an insufficient decline in bedtime OBT were observed in LOW. Sympathetic nervous system activity was significantly higher, while parasympathetic nervous system activity was significantly lower in LOW versus C. Daily physical activity was significantly lower in LOW versus C. Our results suggest that reduced parasympathetic nervous system activity and a lower level of physical activity may affect OBT circadian rhythm. Our data also suggest that a low waking OBT may be associated with delayed OBT circadian rhythm.