BackgroundSeveral studies have suggested an association between major depressive disorder (MDD) and abnormal brain structure. However, it is unclear whether MDD affects cortical gray matter volume, a common indicator of cognitive function. We aimed to determine whether MDD was associated with decreased cortical gray matter volume (GMV) through a Mendelian randomization (MR) study. MethodsWe obtained summary genetic data from a study conducted by the Psychiatric Genomics Consortium, which recruited a total of 480,359 participants (135,458 cases and 344,901 controls). Genetic tools—single nucleotide polymorphisms (SNPs)—of MDD were extracted from the study and their effects on gray matter volumes of the cortex and total brain were evaluated in a large cohort from the UK Biobank (n = 8427). The effects of the SNPs were pooled using inverse variance weighted (IVW) analysis and further tested in several sensitivity analyses. We tested whether C-reactive protein (CRP) levels and interleukin-6 signaling were the mediators of the effects using a multivariate MR model. ResultsThirty-three SNPs were identified and adopted as genetic tools for predicting MDD. IVW analysis showed that MDD was associated with lower overall GMV (beta value −0.106, 95%CI -0.188 to −0.023, p = 0.011) in the frontal pole (left frontal pole, −0.152, 95%CI -0.177 to −0.127, p = 0.013; right frontal pole, −0.133, 95%CI -0.253 to −0.013, p = 0.028). Multivariate and mediation analysis showed that interleukin-6 was an important mediator of GMV reduction. Reverse causality analysis found no evidence that total GMV affected the risk of MDD, but showed that increased left precuneus cortex volume and left posterior cingulate cortex volume were associated with increased risk of MDD. LimitationsPotential pleiotropic effects and overestimation of real-world effects. Key assumptions for MR analysis may not be satisfactorily met. ConclusionMDD was associated with a reduced GMV, and interleukin-6 might be a mediator of GMV reduction.