BACKGROUND: Pregnancy and childbirth are significant events in many women's lives, and the prevalence of depressive symptoms increases during this vulnerable period. Apart from well documented cognitive, affective, and somatic symptoms, stress and depression are associated with physiological changes, such as reduced heart-rate variability (HRV) and activation of the inflammatory response system. Mindfulness Based Interventions may potentially have an effect on both HRV, inflammatory biomarkers, and self-assessed mental health. Therefore, the aim of this study was to assess the effects of a Mindfulness Childbirth and Parenting (MBCP) intervention on HRV, serum inflammatory marker levels, through an RCT study design with an active control group. METHODS: This study is a sub-study of a larger RCT, where significant intervention effects were found on perinatal depression (PND) and perceived stress. Participants were recruited through eight maternity health clinics in Stockholm, Sweden. In this sub-study, we included altogether 80 women with increased risk for PND, and blood samples and HRV measures were available from 60 of the participants (26 in the intervention and 34 in the control group). RESULTS: Participants who received MBCP reported a significantly larger reduction in perceived stress and a significantly larger increase in mindfulness, compared to participants who received the active control treatment. However, in this sub-study, the intervention had no significant effect on PND, inflammatory serum markers or measures of HRV. CONCLUSIONS: No significant differences were found regarding changes in HRV measures and biomarkers of inflammation, larger studies may be needed in the future. TRIAL REGISTRATION: ClinicalTrials.gov ID:  NCT02441595 . Registered 12 May 2015 - Retrospectively registered.