Insomnia is a condition that affects the nervous and muscular system. Thirty percent of the population between 18 and 60 years suffers from insomnia. The effects of this disorder involve problems such as poor school or job performance and traffic accidents. In addition, patients with insomnia present changes in the cardiac function during sleep. Furthermore, the structure of electroencephalographic A-phases, which builds up the Cyclic Alternating Pattern during sleep, is related to the insomnia events. Therefore, the relationship between these brain activations (A-phases) and the autonomic nervous system would be of interest, revealing the interplay of central and autonomic activity during insomnia. With this goal, a study of the relationship between A-phases and heart rate fluctuations is presented. Polysomnography recording of five healthy subjects, five sleep misperception patients and five patients with psychophysiological insomnia were used in the study. Detrended Fluctuation Analysis (DFA) was used in order to evaluate the heart rate dynamics and this was correlated with the number of A-phases. The results suggest that pathological patients present changes in the dynamics of the heart rate. This is reflected in the modification of A-phases dynamics, which seems to modify of heart rate dynamics.