Background: While a growing literature links cardiac autonomic dysregulation to a variety of psychiatric disorders, the relationship between cardiac autonomic functioning and specific symptoms in schizophrenia (SZ) and bipolar disorder (BD) remains elusive. Thus, we investigated heart rate variability (HRV), a proxy for vagal activity, as a biological marker for disease severity in patients with SZ and BD. Methods: HRV was calculated in 35 patients with SZ and 52 patients with BD, as well as in 146 healthy controls. In the patient groups, disease severity and function were measured by the Positive and Negative Syndrome Scale (PANSS) and the Global Assessment of Functioning (GAF) scale. Results: HRV was significantly lower in both clinical groups compared to the healthy controls, with no HRV differences between patient groups. PANSS general psychopathology scores, GAF symptom scores, and GAF function scores showed statistically significant associations with HRV across groups. Conclusions: These results suggest that disease severity is associated with autonomic dysfunction. Thus, HRV may provide a potential biomarker of disease severity in SZ and BD.