Post-traumatic stress disorder (PTSD) symptoms are highly prevalent among individuals with substance use disorders (SUD), presenting a difficult-to-treat, complex comorbidity. Prognostic factors for treatment outcomes may characterize heterogeneity of the treated population and/or implicate mechanisms of action that are salient for improving treatments. High frequency heart rate variability (HF-HRV) is a suggested biomarker for emotion regulation-the ability to generate appropriate emotional responses via the influence of the parasympathetic nervous system on the heart. This initial study investigated the utility of baseline resting HF-HRV for predicting PTSD symptoms and substance use outcomes following treatment of 37 SUD participants with comorbid PTSD symptoms. Participants completed either standard cognitive- behavioral therapy (CBT) for SUD or a novel treatment of integrated post-traumatic stress and substance use that combined CBT for SUD with cognitive processing therapy for PTSD. Analyses demonstrated that higher HF-HRV predicted greater reduction in PTSD symptoms following both types of treatment. This suggests prognostic value of HF-HRV as a predictor of PTSD treatment outcomes; those with poorer autonomic emotional regulation may not respond as well to psychotherapy in general. This hypothesis-generating analysis identifies a putative biomarker that might have utility in treatment prediction.