Anorexia nervosa (AN) patients may present with cardiac autonomic system dysfunction. Power spectral analysis of heart rate variability (HRV) is a reliable noninvasive examination for the quantitative assessment of the central sympathovagal interaction that modulates cardiovascular autonomic function. In the present study, HRV parameters were assessed in female adolescent AN inpatients in the malnourished phase at admission, at discharge when achieving weight restoration, and 24-36 months after discharge, when considered remitted. Nineteen normal-weight female controls were similarly assessed. Spectral analysis of HRV was done with the fast Fourier transform algorithm. At admission and discharge, patients underwent routine laboratory examinations and responded to questionnaires assessing eating-related preoccupations, behaviors, and personality attributes, depression and anxiety. Compared with the controls, AN patients had significantly lower heart-rate and HRV, lower total power and low frequency components, elevated high frequency components, and decreased low to high frequency power ratio as assessed with the power spectral analysis at all three evaluation points. These disturbances were not correlated with the baseline laboratory and psychometric measures. Our preliminary findings suggest that female adolescent AN inpatients may have a cardiovascular autonomic dysfunction in the form of vagal abnormality present not only in malnourished patients, but also persisting following short-term and long-term weight restoration.