Heart rate (HR) variability (HRV) during ambulatory recordings may be affected by individual differences in daily physical activity (PA). However, the influence of various levels of PA on different measures of HRV is not exactly known. We examined the association between simultaneously measured HRV and objective PA data obtained with an accelerometer during waking hours among 45 healthy adults. Bouts of PA were identified from minute-by-minute accelerometer data as metabolic equivalent (METs) values and calculated as mean METs for 30 min. HRV was analyzed concurrently. Within-individual correlation analyses and sign tests were performed to study the relationships between various HRV indexes and PA. The mean PA time was 15:44 +/- 1:01 h, and the mean MET was 1.91 +/- 0.14. HR and sample entropy, but not the other measures of HRV, had a significant relationship with PA, as shown by both correlation analyses (r = 0.64, P = 0.021, and r = -0.55, P = 0.022, respectively) and sign tests (P < 0.0001 for both). Beat-to-beat R-R interval fluctuation expressed as SD1 also demonstrated a significant relation to PA according to the sign test (P = 0.037) and a trend of association according to the correlation analysis (r = -0.40, P = 0.129). The complexity measure of HRV, in addition to average HR and the short-term index of HRV (SD1), is significantly influenced by the level of PA during ambulatory conditions. Long-term HRV indexes remained relatively stable at various activity levels, making them the most robust indexes for the assessment of cardiac autonomic function during free-running ambulatory conditions.