Aims <p>We aimed to compare heart rate variability (HRV) between adolescents with type 1 diabetes and healthy age- and sex-matched control participants. We were also interested in how HRV may change during puberty.</p> Research design and methods <p>Eighty-five adolescents with type 1 diabetes (mean diabetes duration 7.0 ± 3.6 years) and 103 healthy age- and sex-matched youths consented to this cross-sectional study. We derived HRV data for time domain and power spectra analyses from Holter recordings (mean duration 17.8&#xa0;h) and analyzed associated risk factors for HRV deterioration during total recording time and nighttime separately.</p> Results <p>Total low frequency (LF) and very low frequency (VLF) domains (ms²) were significantly lower in children with type 1 diabetes than in healthy controls (LF, <i>P</i> = 0.049 and VLF, <i>P</i> = 0.005, respectively), whereas no differences were found in the measurements taken at night. The most significant predictors for untoward changes in power spectra were skinfold sum and lipids. Mean heart rate (beats/min), or any of the time domain variables did not differ significantly between study groups. Compared with those in the lowest HbA1c tertile, adolescents with type 1 diabetes in the highest HbA1c tertile had significantly lower LF and VLF power spectra results.</p> Conclusions <p>Adolescents with type 1 diabetes have depressed HRV from low to very low frequencies. Deterioration of autonomic nervous system function in adolescents with type 1 diabetes, measured with HRV power spectra is mainly associated with metabolic factors, although it is not possible to establish causal links between these variables.</p>