BackgroundStructural abnormalities in the brain of patients with atopic dermatitis (AD) have been reported; however, the cause has not been determined yet. Herein, we used Mendelian randomization (MR) to reveal the causal effect of AD on brain structure.MethodsThis study utilized summary statistics from genome‐wide association studies (GWASs) to investigate a collection of cerebral structural measures, encompassing cortical thickness (CT), cortical surface area (CA), and subcortical volumes in T1 images. A comprehensive GWAS meta‐analysis identified a total of 20 independent single nucleotide polymorphisms linked to AD, surpassing the genome‐wide significance threshold (p < 5 × 10⁻⁸). MR estimates were aggregated through the application of the inverse variance weighted method. Additional complementary analyses (i.e., MR‐Egger and weighted median approaches) were conducted to further assess the robustness of the obtained results. Sensitivity analysis and multivariate MR (MVMR) while adjusting for brain structural changes risk factors (i.e., depression and anxiety) were performed to assess the reliability and stability of observed causality.ResultsGenetically determined AD exhibited a causal link with reduced caudate volumes (IVW‐MR: β = ‐0.186, p = 0.001, p‐corrected = 0.009). Furthermore, we identified potential causal associations between AD and reduced CT in the cingulate region (posterior cingulate, IVW‐MR: β = ‐0.065, p = 0.018, p‐corrected = 0.551; isthmus cingulate, IVW‐MR: β = ‐0.086, p = 0.003, p‐corrected = 0.188), as well as abnormal cortical surface area (CA) in the supramarginal (IVW‐MR: β = ‐0.047, p = 0.044, p‐corrected = 0.714) and isthmus cingulate (IVW‐MR: β = 0.053, p = 0.018, p‐corrected = 0.714). Additional supplementary analyses yielded consistent outcomes. There was no evidence of horizontal pleiotropy. MVMR analysis showed that the causal effects of AD on abnormal brain structure remained significant while adjusting for depression and anxiety.ConclusionThis MR study provided suggestive evidence that decreased caudate nucleus, posterior cingulate cortex, isthmus cingulate cortex and supramarginal gyrus are suggestively associated with higher AD risk. Future investigation into the brain regions is recommended, which helps to clarify the underlying mechanisms and point to new therapies against AD.