Elevated resting heart rate (RHR) and reduced heart rate variability (HRV) are signs of autonomic nervous system dysfunction identified in schizophrenia (SCZ). This dysfunction has been found to manifest prior to the onset of the clinical diagnosis. Yet whether such autonomic dysfunction is associated with vulnerability to schizophrenia remains unknown. This case-control study included recent onset SCZ patients (n = 35) and healthy controls (HC) (n = 33). Patients were scored for self-disorders (SD's) using the EASE manual and all participants underwent a 5-minute resting state electrocardiogram (ECG) recording. Patients were included from outpatient clinics in Denmark. The main measures comprised EASE total scores (SDs), RHR (beats per minute) and three standard HRV measures usually included in testing autonomic nervous system dysfunction: root mean squared of successive differences (RMSSD), standard deviation of normal-to-normal interval (SDNN) and high-frequency/ low frequency ratio (HF/LF). Pearson correlations and linear regression models adjusted for age, sex and medication were used in the SCZ group. The main finding was a positive moderate association between SDs and RHR (r = 0.463; p = 0.005) and a negative association between SDs and HRV (RMSSD) (r = −0.440; p = 0.008) in the SCZ group. Linear regression models found SDs to explain 22 % of the variance of RHR and 19 % in RMSSD. SDs correlated with LF/HF (r = 0.434; p = 0.009), but non-significantly with SDNN. The study provides evidence of an intriguing link between SDs as a susceptibility trait for schizophrenia spectrum disorders and altered cardiac autonomic functioning.