Background: Alterations in brain cortical structures have been observed in patients with immune diseases, but the causal relationship remains unclear. This study employs Mendelian randomization (MR) to investigate the causal effects of immune diseases on brain cortical structures. Methods: Genome-wide association studies (GWAS) summary data for immune diseases were utilized. Additionally, data from 51,665 participants in the ENIGMA Consortium were analyzed to assess the link between genetic predisposition to immune diseases and changes in cortical thickness (TH) and surface area (SA). Magnetic resonance imaging (MRI) measured SA and TH globally and in 34 functional brain regions. Inverse-variance weighted (IVW) analysis was the primary method, with MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO), MR-Egger, and weighted median methods used to detect heterogeneity and pleiotropy. Findings: Globally, there was no significant causal relationship between immune diseases and overall brain cortex structure. However, at the regional level, many immune diseases were found to affect cortical areas linked to cognitive impairment, particularly osteoarthritis and gout. No pleiotropy was detected. Interpretation: Immune diseases have a causal influence on cortical structure, suggesting the existence of an immune-brain axis.