Literature reports on the very high frequency (VHF) range of 0.4–0.9 Hz in heart rate variability (HRV) are scanty. The VHF presence in cardiac transplant patients and other conditions associated with reduced vagal influence on the heart encouraged us to explore this spectral band in healthy subjects and in patients diagnosed with cardiac autonomic neuropathy (CAN), and to assess the potential clinical value of some VHF indices. The study included 80 healthy controls and 48 patients with spinocerebellar ataxia type 2 (SCA2) with CAN. The electrocardiographic recordings of short 5-min duration were submitted to three different spectral analysis methods, including the most generally accepted procedure, and the two novel methods using the Hilbert-Huang transform. We demonstrated the presence of VHF activity in both groups of subjects. However, VHF power spectral density, expressed in relative normalized units, was significantly greater in the SCA2 patients than that in healthy subjects, amounting to 36.1 ± 17.4% vs. 22.9 ± 14.1%, respectively, as also was the instantaneous VHF spectral frequency, 0.58 ± 0.05 vs. 0.64 ± 0.07 Hz, respectively. These findings were related to the severity of CAN. We conclude that VHF activity of HRV is integral to the cardiovascular autonomic control.