Increased risk of cardiovascular diseases and autonomic dysregulation are common health concerns in individuals with spinal cord injury (SCI). Two therapies that may help improve cardiovascular control are body-weight supported treadmill training (BWSTT) and head-up tilt training (HUTT). The purpose of this study was to examine the effects of short-term BWSTT and HUTT on cardiac autonomic function. Seven participants (6 male, 37.1+/-7.7 years) with SCI (C5-T10, ASIA A-C; 5.0+/-4.4 years post-injury) completed the study protocol. In this randomized cross-over design, participants were required to complete 4 weeks of thrice-weekly BWSTT and HUTT (i.e. 12 sessions each), separated by a 4 week detraining period. Cardiac autonomic function was assessed at rest, before and after, each 4 week training period using linear and non-linear measures (sample entropy and detrended fluctuation analysis (alpha(1))) of heart rate dynamics. Participants completed equivalent amounts of time performing BWSTT and HUTT (453.7+/-27.3 min vs. 471.6+/-19.7 min, p=0.24). There were no significant differences in linear heart rate variability following BWSTT or HUTT (p>0.05). In contrast, there was a significant change in sample entropy following BWSTT (1.05+/-0.14 to 1.42+/-0.12, p<0.05). Due to the bi-directional pattern of alpha(1) values, distance scores were calculated (|1-alpha(1)|) and demonstrated a significant reduction following BWSTT (0.54+/-0.06 to 0.26+/-0.05, p=0.001). In conclusion, 4 weeks of BWSTT but not HUTT training are sufficient to increase sample entropy and reduce the fractal scaling distance score in participants with SCI.