Previous studies have suggested a possible link between autoimmune diseases and graft dysfunction; however, a causal link remains unclear. Exposure factors were set as 13 autoimmune diseases, and outcomes were set as graft dysfunction. Mendelian randomization was used to analyze the causal link between exposure and outcome. Alopecia areata and asthma were linked to graft dysfunction (odds ratio 0.828; 95% confidence interval 0.699–0.980; P = .029; odds ratio 1.79; 95% confidence interval 1.069–2.996; P = .027). At the same time, primary sclerosing cholangitis was found to be heterogeneous as an exposure factor (P = .009), but no heterogeneity or pleiotropy was found in other exposure factors. Our preliminary findings show 2 autoimmune diseases as risk factors for graft dysfunction, 1 autoimmune disease as a protective factor for graft dysfunction and the mechanisms remain to be understood.