Objectives: Senility death is defined as natural death in the elderly who do not have a cause of death to be described otherwise and, if human life is finite, it may be one of the ultimate goals of medicine and healthcare. A recent survey in Japan reports that municipalities with a high senility death ratio have lower healthcare costs per late-elderly person. However, the causes of regional differences in senility death ratio and their biomedical determinants were unknown. In this study, we examined the relationships of the regional difference in senility death ratio with the regional differences in heart rate variability and physical activity. Methods: We compared the age-adjusted senility death ratio of all Japanese prefectures with the regional averages of heart rate variability and actigraphic physical activity obtained from a physiological big data of Allostatic State Mapping by Ambulatory ECG Repository (ALLSTAR). Results: The age-adjusted senility death ratio of 47 Japanese prefectures in 2015 ranged from 1.2% to 3.6% in men and from 3.5% to 7.8% in women. We compared these ratios with the age-adjusted indices of heart rate variability in 108,865 men and 136,536 women and of physical activity level in 16,661 men and 21,961 women. Heart rate variability indices and physical activity levels that are known to be associated with low mortality risk were higher in prefectures with higher senility death ratio. Conclusion: The regional senility death ratio in Japan may be associated with regional health status as reflected in heart rate variability and physical activity levels.