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Abstract Background Obesity is associated with reduced heart rate variability (HRV), reflecting detrimental changes in cardiac regulation by the autonomic nervous system (ANS). Weight loss reverses this change and ANS dysfunction is thought to have a role in obesity-related cardiac pathology. Few studies have examined the influence of weight-reduction (bariatric) surgery on cardiac autonomic control. This study therefore sought to assess longitudinal changes in indices of cardiac autonomic control following two types of bariatric procedure, laparascopic gastric banding (LGB) and biliopancreatic diversion (BPD). Methods Eleven morbidly obese subjects aged 47.8 ± 7.9 years (mean ± SD) with BMI 48.2 ± 6.9 kg·m - 2 underwent weight-reduction surgery: five received BPD and six received LGB. Holter ECG was recorded and HRV was quantified together with a QT variability index (QTVI), a complexity index (SampEn), and a fractal (scaling) index (DFAα). Repeated measures ANOVA compared the indices for the two groups as a function of time (1, 6 and 12 months follow-up). Results BMI was reduced by up to 24% (p = 0.008) post-surgery despite patients remaining obese at one-year follow-up. Several indices showed prompt and persistent improvement with progressive weight loss, QTVI being the most sensitive discriminator of recovery time (F3,216 = 16.86; p < 0.0005; η2 = 0.190). Autonomic responsiveness was functionally normal throughout. The bariatric procedures induced similar changes in cardiac autonomic control, despite their differing mechanisms of action. Conclusions This pilot study suggests that the mechanism responsible for improving cardiac regulation following bariatric surgery might be the weight loss itself. Furthermore, post-surgery improvement in QTVI implies that weight loss reduces the risk of ventricular arrhythmic events.