Previous meta-analyses of structural MRI studies have shown diffuse cortical and sub-cortical abnormalities in unipolar depression. However, the presence of duplicate publications, recruitment of particular age groups and the selection of specific regions of interest means that there is uncertainty about the balance of current research. Moreover, the lack of systematic exploration of highly significant heterogeneity has prevented the generalisability of finding. A systematic review and random-effects meta-analysis was carried out to estimate effect sizes. Possible publication bias, and the impact of various study design characteristics on the magnitude of the observed effect size were systematically explored. The aim of this study was 1) to include structural MRI studies systematically comparing unipolar depression with bipolar disorder and healthy volunteers; 2) to consider all available structures of interest without specific age limits, avoiding data duplication, and 3) to explore the influence of factors contributing to the measured effect sizes systematically with meta-regression analyses. Unipolar depression was characterised by reduced brain volume in areas involved in emotional processing, including the frontal cortex, orbitofrontal cortex, cingulate cortex, hippocampus and striatum. There was also evidence of pituitary enlargement and an excess of white matter hyperintensity volume in unipolar depression. Factors which influenced the magnitude of the observed effect sizes were differences in methods, clinical variables, pharmacological interventions and sample age.