Autonomic cardiac control of children with diabetes mellitus (DM, n = 12), juvenile rheumatoid arthritis (JRA, n = 12) and healthy controls (n = 12) was studied by a procedure consisting of a deep breathing test and an intermittent tilting test. Frequency selective entrainment of HR could be produced by tilting and deep breathing. No statistically significant intergroup differences were detected in the patterns of average heart rate (HR), overall or beat-to-beat heart rate variability (HRV) or HRV spectra. The DM group had an 8% higher HR and a limited short-term HRV response in relation to HR throughout the whole test procedure compared to controls. This increased HR causes an extra load to the cardiovascular system. We conclude that in spite of elevated HR and changed short-term chronotropic HR control in DM no features of autonomic failure could be detected in children with JRA.