The diagnostic assessment of autism spectrum disorders (ASD) in adults is a challenging and time-consuming procedure. In order to address the lack of specialised health-care professionals and improve the waiting time, we aimed to identify specific electrocardiogram (ECG) derived Heart Rate Variability (HRV) parameters that could be used for diagnostic purposes. 152 patients were diagnosed based on a standardised clinical procedure and assigned to one of three groups: ASD (n = 56), any other psychiatric disorder (OD) (n = 72), and patients with no diagnosis (ND) (n = 24). Groups were compared using ANOVA. Discriminative power of biological parameters and the clinical assessment were compared using receiver operating characteristic curves (ROCs). Patients with ASD showed reduced parasympathetic and increased sympathetic activity compared to ND. The accuracy determined by the area under the curve (AUC) of the biological parameters for discrimination between ASD vs. pooled OD/ND was 0.736 (95% CI = 0.652-0.820), compared to .856 (95% CI = 0.795-0.917) for the extensive clinical assessment. Our results confirmed the dysregulation of the autonomic nervous system in ASD with reduced parasympathetic and increased sympathetic activity as compared to ND. The discriminative power of biological markers including HRV was considerable and could supplement less sophisticated clinical assessments.