Our study was designed to investigate and quantitatively characterise the interaction of breathing and instantaneous heart rate. Comparisons were made during consciousness at rest, and during non-REM sleep. 31 12-14-year-old healthy children were subjected to a 24-h polygraphic electrocardiogram, respirogram, electrooculogram and actogram measurements. The data were analysed by means of power spectral analysis and coherence spectra. The peak frequency of high-frequency heart rate fluctuations was always clearly related to the breathing frequency, i.e., respiratory sinus arrhythmia is present in both states. Moving squared coherence analysis demonstrates the stability of the cardiorespiratory coupling to remain constant during wakefulness or non-REM sleep. However, coherence increases from waking state to non-REM sleep. The lower coherence during waking state may be explained by greater additional central and peripheral influences on the cardiorespiratory coupling or by increased non-linear properties of the transfer system due to operating point shifting.