Earlier studies have indicated that patients claiming to be sensitive to electromagnetic fields, so-called electrical hypersensitivity (EHS), have a dysbalance of the autonomic nervous system (ANS) regulation. This paper focuses on a possible dysbalance in the ANS among EHS patients by the use of long-term monitoring of electrocardiogram (ECG) in both a patient and a matched control group. At the same time, the environmental power frequency magnetic field was recorded for both groups in order to see if there was any difference in exposure between the groups. ECG, heart rate (HR) and heart rate variability (HRV) as well as the magnetic field exposure were monitored for 24 h. Fourteen patients with perceived EHS symptoms were selected from the University Hospital, Umeå, Sweden. Symptoms indicating autonomic nervous dysregulation were not part of the inclusion criteria of the patient group. Age and sex matched healthy subjects were used as controls. No differences were found between the groups regarding magnetic field exposure or the mean HR for 24 h. The HRV analyses showed that the high-frequency (HF) component did not have the expected increase with sleep onset and during nighttime in the EHS group. When separating the sleeping and awake time even less differences between the two conditions in the EHS patients, both for the low-frequency and HF components in the HRV spectrum, were seen. EHS patients had a disturbed pattern of circadian rhythms of HRV and showed a relatively 'flat' representation of hourly-recorded spectral power of the HF component of HRV.