Cardiac vagal tone, indexed by heart rate variability (HRV), is a proxy for the functional integrity of feedback mechanisms integrating central and peripheral physiology. To quantify differences in HRV in individuals with schizophrenia compared with healthy controls. Databases were systematically searched for studies eligible for inclusion. Random effect meta-analyses of standardised mean differences were calculated for vagal activity indicated by high-frequency HRV and the root mean square of successive R-R interval differences (RMSSD). Thirty-four studies were included. Significant main effects were found for high-frequency HRV (P = 0.0008; Hedges' g = -0.98, 95% CI -1.56 to -0.41, k = 29) and RMSSD (P<0.0001; g = -0.91, 95% CI -1.19 to -0.62, k = 24), indicating lower vagal activity in individuals with schizophrenia than in healthy controls. Considerable heterogeneity was evident but effects were robust in subsequent sensitivity analyses. Given the association between low HRV, threat processing, emotion regulation and executive functioning, reduced vagal tone may be an endophenotype for the development of psychotic symptoms.