Background: Eating disorders such as anorexia nervosa present with a significant cardiovascular associated risk of sudden cardiac death. Bradycardia is a serious complication of eating disorders. Methods: Eating Disorder (ED) patients were admitted to a 6-week treatment program and assessed for of heart rate variability (HRV) at entrance to the program and at discharge from hospital. Linear heart rate variability measures were determined using Kubios software from Lead 3 ECG recordings following a 5-minute rest period. Nonparametric statistics were applied and significance set at p < 0.05.Results: No significant differences in HRV parameters were noted for the control group following the 6-week treatment program. For the ED group, mean RR interval length decreased significantly following treatment (median ±IQR; -64 ± 76; p = 0.002). Sympathovagal function was abnormal in the ED group on admission but improved following treatment, showing a decrease in RMSSD (median ± IQR; -9 ± 18; p = 0.048) and SD1 (median ± IQR; -6 ±13; p = 0.048). Sample entropy, a, measure of heart rate complexity did not change significantly. Conclusion: At admission to hospital the ED group was more parasympathetic during rest compared to controls,but they became more sympathetic after the intervention and approached the HRV measures of the controls.