The aim of this study was to investigate the cardiovascular autonomic acute response, during recovery after handcycle training, in quadriplegics with spinal cord injury (SCI). [Subjects and Methods] Seven quadriplegics (SCIG -level C6-C7, male, age 28.00 +/- 6.97 years) and eight healthy subjects (CG -male, age 25.00 +/- 7.38 years) were studied. Their heart rate variability (HRV) was assessed before and after one handcycle training. [Results] After the training, the SCIG showed significantly reduced: intervals between R waves of the electrocardiogram (RR), standard deviation of the NN intervals (SDNN), square root of the mean squares differences of sucessive NN intervals (rMSSD), low frequency power (LF), high frequency power (HF), and Poincare plot (standard deviation of short-term HRV -SD1 and standard deviation of long-term HRV -SD2). The SDNN, LF, and SD2 remained decreased during the recovery time. The CG showed significantly reduced: RR, rMSSD, number of pairs of adjacent NN intervals differing by more than 50 ms (pNN50), LF, HF, SD1, and sample entropy (SampEn). Among these parameters, only RR remained decreased during recovery time. Comparisons of the means of HRV parameters evaluated between the CG and SCIG showed that the SCIG had significantly lower pNN50, LF, HF, and SampEn before training, while immediately after training, the SCIG had significantly lower SDNN, LF, HF, and SD2. The rMSSD30s of the SCIG significantly reduced in the windows 180 and 330 seconds and between the windows 300 seconds in the CG. [Conclusion] There was a reduction of sympathetic and parasympathetic activity in the recovery period after the training in both groups; however, the CG showed a higher HRV. The parasympathetic activity also gradually increased after training, and in the SCIG, this activity remained reduced even at three minutes after the end of training, which suggests a deficiency in parasympathetic reactivation in quadriplegics after SCI.