Autonomic function tests require standardised test conditions. We compared testing under non-standardised and standardised conditions and investigated the agreement between heart and pulse rate variability in 30 subjects with diabetes mellitus. Deep breathing, Valsalva manoeuvre and quick standing tests showed non-standardised reproducibility intraclass correlations (95% CI) of 0.96 (0.82-0.99), 0.96 (0.81-0.99) and 0.75 (-0.98 to 0.94), respectively. Intraclass correlations for sustained handgrip and quick standing were poor. Heart and pulse rate variability showed high-frequency band intraclass correlations (95% CI) of 0.65 (-0.07 to 0.89) and 0.47 (-0.88 to 0.85) for the very low-frequency band, respectively, 0.68 (0.00-0.90) and 0.70 (-0.09 to 0.91) for the low-frequency band, and 0.86 (0.57-0.95) and 0.82 (0.39-0.95) for the high-frequency band. Reproducibility under standardised conditions was comparable. The mean difference (95% limits of agreement) between heart and pulse rate variability was 0.99 (0.80-1.22) for very low frequency, 1.03 (0.88-1.21) for low frequency and 1.35 (0.84-2.16) for high frequency, with a Spearman's correlation coefficient of 1.00, 0.99 and 0.98, respectively. We demonstrated a high agreement between heart and pulse rate variability and acceptable reproducibility with most autonomic function tests, heart and pulse rate variability.