Previous results on heart rate variability (HRV) analysis in anorexia nervosa (AN) include some apparently conflicting data. In order to find out the reason for different results and to improve understanding of autonomic control in AN we compare HRV in acute and chronic AN. Spectral powers, fractal scaling exponent and sample entropy were computed from 24 h RR series derived from Holter ECG recordings in 17 anorexic patients, nine chronic and eight healthy women. We found that all linear and non-linear HRV measures change in different direction in acute and chronic AN. Acute AN is characterized by decreased HR and increased HRV. In chronic AN, HR is increased, HRV reduced and the difference between awake and sleeping values is high. HRV measures are associated with body mass index only in chronic AN. As HRV measures are significantly different between acute and chronic AN, we propose that HRV analysis might provide additional data in clinical practice.