Heart rate shows a circadian rhythm. This has not yet been sufficiently investigated for its variability till now, which challenges the analysis of rhythms of the variability and their validity in long time records. For this purpose, time series of heart period duration (HPD) and sinus arrhythmia (SA) were measured in 30 children in a boarding-school (14 male, 16 female, 12 to 14 years of age) from the ECG for 5 min/h during 24 h. Fast Fourier transform provided the spectra and the power density. HPD, SA, power maxima and their frequencies were analyzed for circadian rhythms according to Halberg. Times of meals and sleep were uniform. Power and frequencies of the spectra showed individual patterns, stable throughout the day in 2 diverse groups. SA, high- (HF) and middle frequent (MF) spectral parts show circadian oscillations in frequency or power with acrophases during day or night, often in contrast to HF and MF. This proves the existence of circadian rhythms of heart rate variability for SA, HF and MF. In some cases, the individual 24-h patterns are superimposed by effects of external zeitgeber, e.g. meals.