Individuals with spinal cord injury (SCI) show alterations in the autonomic regulation at rest which can affect the heart rate variability (HRV) during exercise. The aim of this study was to compare the HRV threshold of a group with SCI with two control groups. Twenty-four men, seven with SCI (24.8 ± 2.0 years, 76.5 ± 6.9kg, 176.3 ± 1.9cm), eight sedentary subjects without SCI (CONSED) (24.1 ± 1.8 years, 75.1 ± 3.6kg, 176.3 ± 3.0cm) and nine athletes without SCI (CONATH) (22.6 ± 1.4 years, 73.8 ± 5.3kg, 175.6 ± 2.5cm) volunteered in this study. The participants performed an upper limb incremental test on a cycle ergometer (17.2W/two minutes) until exhaustion. The SD1 index of HRV was measured every stage, and the HRV threshold was identified at: 1) the first workload that elicited SD1 values lesser than 3ms; 2) the first stage that elicited a difference between SD1 values from two consecutive stages lesser than 1ms. SD1 values at rest or at 30% of Wmax were higher (p < 0.05) in CONSED (45.8 ± 6.8ms) than CONATH group (19.5 ± 4.4ms) but none of them were different (p > 0.05) from group SCI (25.8 ± 4.5ms). The 3ms HRV threshold expressed in absolute values or in relative to maximal workload and heart rate was not different between groups. However, the workload of 1ms HRV threshold in control group (68.8 ± 8.3W) was significantly higher (p < 0.05) than SCI group (21.5 ± 4.3W), but these groups were not different from CONSED group (41.3 ± 8.7W). These results suggest changes in autonomic control during exercise in subjects with SCI, which might lead to an early parasympathetic withdrawal during incremental exercise.