BACKGROUND: Many studies have reported disturbances of heart rate variability (HRV) in patients with psychosomatic disorders such as anorexia nervosa (AN) and the irritable bowel syndrome (IBS). However, both have never been directly compared. METHODS: We compared HRV in AN (n = 21) and in IBS (n = 21) (all females) with 42 healthy female control subjects who were matched for age and in IBS to body mass index (BMI). Recovery periods between different cardiac load tests were compared with baseline recordings and tilt test to estimate time [mean successive difference (MSD)] and frequency domain (Goldberger dimension, frequency of HF peak location and HF power, log HF power) values and to assess general reactivity of the autonomic nervous system (ANS). KEY RESULTS: Significantly longer inter-beat intervals (IBIs) in AN patients and lower values of MSD in IBS patients were found in comparison with respective controls; both were independent from experimental conditions and are found in baseline recordings only. Both effects were independent of age and BMI. We also demonstrate a significant relationship between age, BMI and some HRV parameters. CONCLUSIONS & INFERENCES: Opposite autonomic patterns were found in AN and IBS: stronger vagal withdrawal in IBS and weaker vagal inhibition in AN patients. Records made at rest and without any autonomic load may be representative for assessment of ANS function. Age and BMI should be taken into consideration during assessment of HRV data.