OBJECTIVE: Coronary artery bypass grafting (CABG) is accompanied by severe impairment of cardiac autonomous regulation (CAR). This study aimed to determine whether a short-term physiotherapy exercise protocol post-CABG, during inpatient cardiac rehabilitation (CR), might improve CAR. DESIGN: Seventy-four patients eligible for CABG were recruited and randomised into physiotherapy exercise group (EG) or physiotherapy usual care group (UCG). EG patients underwent a short-term supervised inpatient physiotherapy exercise protocol consisting of an early mobilisation with progressive exercises plus usual care (respiratory exercises). UCG only received respiratory exercises. Forty-seven patients (24 EG and 23 UGC) completed the study. Outcome measures of CAR included linear and non-linear measures of heart rate variability (HRV) assessed before discharge. RESULTS: By hospital discharge, EG presented significantly higher parasympathetic HRV values [rMSSD, high frequency (HF), SD1)], global power (STD RR, SD2), non-linear HRV indexes [detrended fluctuation analysis (DFA)alpha1, DFAalpha2, approximate entropy (ApEn)] and mean RR compared to UCG (p<0.05). Conversely, higher values of mean HR, low frequency (LF) (sympathetic activity) and the LF/HF (global sympatho-vagal balance) were found in the UCG. CONCLUSIONS: A short-term supervised physiotherapy exercise protocol during inpatient CR improves CAR at the time of discharge. Thus, exercise-based inpatient CR might be an effective non-pharmacological tool to improve autonomic cardiac tone in patient\'s post-CABG.