Background Effectiveness of heart rate variability (HRV) biofeedback is dependent on the relationship between the measured respiratory-heart rate coherence (C HR) and the resonant frequency (RFB) breathing. C HR is driven by the central autonomic network which consists of the interplay between the components of the autonomic nervous system, brainstem modulatory nuclei and cortical function. The extent to which heart rate is in coherence with respiratory frequency and the function of the central autonomic network in major depressive disorder (MDD) and suicidal ideation (SI) has not been investigated. Method: Sixty-one patients provided informed consent to participate and were divided into no MDD (CONT), MDD and an MDD plus SI (MDDSI) group. HRV activity was determined by multi lag tone-entropy (T-E) and respiratory-C HR at rest was characterized by the relationship between respiratory rate and heart rate. Results: CONT had the highest entropy compared to the MDDSI group, which had the lowest entropy and highest tone (p < 0.05). Autonomic parasympathetic function was also significantly lower in the MDDSI compared to the MDD group (p < 0.05). C HR indicated a significant phase desynchronization (decrease in coherence) between MDDSI, MDD and CONT (p < 0.05), with MDDSI having the lowest coherence and CONT the highest. Conclusion: T-E analysis indicated that HRV was significantly different in patients with SI. C HR as measured by our proposed synchronization index provides a novel feature to adapt HRV biofeedback to individual psychiatric profiles and may provide better clinical outcomes for this patient group.