While facial autonomic signs are prominent during cluster headache (CH) attacks, cardiovascular autonomic changes have been described in few CH patients. Cardiovascular autonomic function tests (AFT) can be used to assess general autonomic function in CH patients in different stages of the disease. We aimed to assess whether general autonomic function is changed in CH patients during a cluster period. AFT was performed both during a cluster period, but outside an actual attack, and outside a cluster period in 18 patients. Heart rate variability was studied at rest, during deep breathing, after standing up and during a Valsalva manoeuvre. Blood pressure (BP) changes were recorded at rest, during standing up and during sustained handgrip. Measurements during and outside the cluster period were compared using the paired t-test. AFT measurements revealed no significant differences between the two measurements, except for diastolic BP in rest, which was higher during the cluster period [80.3 (SD 12.2) vs. 74.8 (SD 9.0), P = 0.04]. Autonomic dysfunction during a cluster period, but outside an attack, does not include systemic cardiovascular control.