BACKGROUND: Whole-body vibration (WBV) is an exercise modality that can promote improvements in heart rate variability (HRV) with lower patient overload, and consequently reduce cardiovascular risk in renal transplant patients. The aim of this study was to evaluate the effects of a 12-week WBV training program of two weekly sessions on HRV. METHODS: A double-blind, randomized controlled clinical trial with 12 kidney transplant recipients of both genders who underwent WBV training (35鈥疕z) twice a week for 12 weeks on alternate days (WBV Group) and training with sub-therapeutic WBV (8鈥疕z) (Sham Group). Variables were evaluated in time and frequency domains of HRV through the 24-h Holter monitor, heart rate (HR), blood pressure (BP) and maximum oxygen consumption (VO(2max)) through an exercise stress test. RESULTS: The delta between Sham and WBV groups showed an increase in the low frequency (Delta鈥?鈥?59.05鈥疕z; p鈥?鈥?.01) and in the high frequency (Delta鈥?鈥?04.42鈥疕z; p鈥?鈥?.04) of the HRV compared to Sham group. No changes in the ergometric variables were observed for any of the groups. CONCLUSION: The present study evidenced an increase in the low and high frequency of HRV in individuals who participated in the Sham WBV group. There was no improvement in the autonomic balance in the groups, in the other HRV parameters, or the exercise test after the WBV training period.