PURPOSE: Adverse effects by night-call duty have become an important occupational health issue. The aim of this study was to investigate whether the heart rate variability (HRV) differed during recovery from day work and night-call duty between distinct physician specialities. METHODS: We studied the impact of a 16-h night-call duty on autonomic balance, measured by HRV, among two physician groups differing with respect to having to deal with life-threatening conditions while on call. Nineteen anaesthesiologists (ANEST) and 16 paediatricians and ear, nose and throat surgeons (PENT) were monitored by ambulatory digital Holter electrocardiogram (ECG). Heart rate variability was analysed between 21:00 and 22:00 after an ordinary workday, on night call and in the evening post-call. Absolute and normalized high-frequency power (HF, HFnu) were the main outcome variables, expressing parasympathetic influence on the heart. RESULTS: ANEST had lower HF power than PENT while on night call and post-daytime work (p < 0.05), but not at post-night call. In the whole group of physicians, HFnu was lower on call and post-daytime work compared with post-night-call duty (p < 0.05). CONCLUSIONS: The physiological recovery after night duty seemed sufficient in terms of HRV patterns for HFnu, reflecting autonomic balance and did not differ between specialities. However, the less dynamic HRV after daytime work and during night-call duty in the ANEST group may indicate a higher physiological stress level. These results may contribute to the improvement of night-call schedules within the health care sector.