The aim of this work is to study the behavior of the autonomic system through variations in the heart rate (HR) during the Cyclic Alternating Pattern (CAP) which is formed by A-phases. The analysis was carried out in 10 healthy subjects and 10 patients with Nocturnal Front Lobe Epilepsy (NFLE) that underwent one whole night of polysomnographic recordings. In order to assess the relation of A-phases with the cardiovascular system, two time domain features were computed: the amplitude reduction and time delay of the minimum of the R-R intervals with respect to A-phases onset. In addition, the same process was performed over randomly chosen R-R interval segments during the NREM sleep for baseline comparisons. A non-parametric bootstrap procedure was used to test differences of the kurtosis values of two populations. The results suggest that the onset of the A-phases is correlated with a significant increase of the HR that peaks at around 4[Formula: see text]s after the A-phase onset, independently of the A-phase subtype and sleep time for both healthy subjects and NFLE patients. Furthermore, the behavior of the reduction in the R-R intervals during the A-phases was significantly different for NFLE patients with respect to control subjects.