Beat-to-beat heart rate (HR) dynamics were studied by plotting each R-R interval as a function of the previous R-R interval (Poincaré plot) during incremental doses of atropine followed by exercise for 10 subjects and during exercise without autonomic blockade for 31 subjects. A quantitative two-dimensional vector analysis of a Poincaré plot was used by measuring separately the standard deviation of instantaneous beat-to-beat R-R interval variability (SD1) and the standard deviation of continuous long-term R-R interval variability (SD2) as well as the SD1/SD2 ratio. Quantitative Poincaré measures were compared with linear measures of HR variability (HRV) and with approximate entropy (ApEn) at rest and during exercise. A linear progressive reduction was observed in SD1 during atropine administration, and it remained almost at the zero level during exercise after a parasympathetic blockade. Atropine resulted in more variable changes in SD2 and the SD1/SD2 ratio, but during exercise after parasympathetic blockade, a progressive increase was observed in the SD1/SD2 ratio until the end of exercise. The SD1/SD2 ratio had no significant correlations with the frequency domain measures of HRV. However, the SD1/SD2 ratio had a modest correlation with ApEn at rest (r = -0.69, P < 0.001), but not during exercise (r = 0.27, P = NS). All measures of vagal modulation of HR decreased progressively until the ventilatory threshold level was reached, when sympathetic activation was reflected as changes in the SD1/SD2 ratio. These results show that quantitative two-dimensional vector analysis of a Poincaré plot can provide useful information on vagal modulation of R-R interval dynamics during exercise that are not easily detected by linear summary measures of HRV or by ApEn.