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Purpose: To assess the impact of bariatric surgery and an added supervised exercise training programme on heart rate variability (HRV) in patients with severe obesity., Methods: Fifty-nine patients who underwent bariatric surgery were randomised in the post-operative period to a 12-week supervised exercise training programme (moderate intensity combination aerobic/resistance exercise training programme) or a control group. Indices of HRV including time-domain, spectral-domain, and nonlinear parameters were measured preoperatively, and at 3, 6, and 12 months., Results: After the surgical procedure, both groups improved anthropometric parameters. Type 2 diabetes, hypertension, and dyslipidemia resolutions were similar between groups. Total body weight loss at 6 and 12 months were also comparable between groups (6 months: 28 ± 6 vs. 30 ± 6%; 12 months: 38 ± 9 vs. 38 ± 10%; control vs. intervention group respectively). Bariatric surgery improved HRV parameters at 12 months compared to the pre-operative values in the intervention group: standard deviation of R-R interval (SDNN) (156.0 ± 46.4 vs. 122.6 ± 33.1 ms), low frequency (LF) (6.3 ± 0.8 vs. 5.8 ± 0.7 ms 2 ), and high frequency (HF) (5.1 ± 0.8 vs. 4.7 ± 0.9 ms 2 ) (all p <0.001). For the control patients, similar improvements in SDNN (150.0 ± 39.4 vs. 118.8 ± 20.1 ms), LF (6.1 ± 0.9 vs. 5.7 ± 0.8 ms 2 ), and HF (5.0 ± 0.9 vs. 4.7 ± 0.9 ms 2 ) were obtained (all p <0.001). However, there was no add-on impact of the supervised exercise training programme on HRV after 12 months ( p >0.05 for all HRV parameters)., Conclusion: Bariatric surgery is associated with an improvement in HRV. A supervised exercise training programme in the post-operative period did not modulate further the benefits of bariatric surgery regarding HRV parameters.