Background:The study compares the impact of cardiac surgical interventions on the autonomic function by assessing the pre-operative status and early post-operative recovery of subjects undergoing isolated mitral valve replacement (MVR), isolated aortic valve replacement (AVR), and transcatheter aortic valve implantation (TAVI). We analyze heart rate variability (HRV), baroreflex sensitivity (BRS), and cardiovascular coupling in a longitudinal, i.e., the temporal evolution of autonomic function within each group before, 1 day after, and 7 days after surgery, and a transversal, i.e., between groups of patients at identical time instants, setting. Results: A total of 243 records from 124 patients (38 MVR, 57 AVR, 29 TAVI) was analyzed. There were no major differences in HRV, BRS, and coupling between the groups in the pre-operative values. Longitudinal analysis proves a depressed autonomic function for MVR and AVR patients after surgery (in MVR patients, p < 0.001 for most parameters related to HRV and BRS), but not for TAVI patients. TAVI patients showed no differences before and after surgery. Transversal analysis reveals the strongest impairments throughout HRV and BRS parameters for MVR patients. In the case of AVR, the autonomic regulation was also depressed, though not to the extent as seen in MVR patients. Cardiovascular coupling by means of symbolic coupling traces (SCT) was shown to be clearly reduced the day after surgery in MVR and AVR patients. In TAVI patients, there was no reduction but already the day after surgery developed additional couplings. Conclusions: Our results prove a characteristic behavior of the autonomic function in relation to the gravity of the surgical procedure. As variables related to the process of the surgical interventions were kept similar between patient groups, direct surgical trauma is assumed to be responsible for the heavy decrease of autonomic function in the case of MVR. TAVI, in contrast, proves to be very suited in terms of maintaining the autonomic function in comparison to AVR. Further studies incorporating larger populations should confirm our findings and relate the autonomic state to malignant events after surgical interventions to build the fundament of a strengthened inclusion of cardiovascular variability and coupling analysis in the pre-, peri-, and post-operative care.