BACKGROUND: Recently there has been increasing interest in the study of ultra-short-term heart rate variability (HRV) in sports performance and exercise physiology. In order to improve standardization of this specific analysis, we evaluated the ultra-short-term HRV analysis through SD1Poincare Index to identify exercise induced responses. METHODS: We investigated 35 physically active men aged between 18 and 35 years old. Volunteers performed physical exercise on treadmill with intensity of 6.0 km/hour + 1% slope in the first five minutes for physical "warming up." This was followed by 25 minutes with intensity equivalent to 60% of maximal oxygen consumption, with the same slope according to the Conconi threshold. HRV was analyzed in the following periods: the five-minute period before the exercise and the five-minute period immediately after the exercise, the five minutes were divided into five segments of 60 RR intervals. Ultra-short-term RMSSD and SD1 analysis were performed. RESULTS: Ultra-short-term RMSSD and SD1 were significantly (P<0.0001) reduced during the initial five minutes divided into five segments of 60 RR intervals compared to (at rest) control. Heart rate was significantly (P<0.0001) increased 1 min and 3 min immediately after exercise compared to (at rest) control. At rest ultra-short-term SD1 presented significant correlation with short-term (256 RR intervals) RMSSD (r=0.78; P<0.0001), HF (r=0.574; P=0.0007) and SD1 (r=0.78; P<0.0001). Additionally, visual analysis with the Poincare plot detected changes in HRV after exercise. CONCLUSIONS: Ultra-short-term HRV analysis through Poincare plot identified heart rate autonomic responses induced by aerobic exercise.