As a physiological big-data project named ALLSTAR, we have developed a 24-hr ambulatory electrocardiogram database of 81,615 males and 103,038 females (≥20 yr) from all over Japan. With this database, we examined if regional differences in heart rate (HR) and HR variability (HRV) are associated with the inter-prefecture rankings of healthy life expectancy (HALE) and of average life expectancy (ALE) in Japan. According to reports by the Japanese Ministry of Health, Labour and Welfare (2013), subjects in each sex were grouped into short, middle, and long HALE and ALE tertiles by their living prefectures. Standard deviation of 24-h normal-to-normal R-R intervals (SDNN) increased progressively with increasing HALE tertiles in both sexes (Ps < 0.001), while it showed no consistent associations with ALE. Conversely, HR decreased progressively with increasing ALE tertiles in females (P < 0.001), while it showed no consistent association with HALE. These suggest HRV may reflect a biological property relating to long HALE.