Objective: To evaluate the association between autoimmune diseases (ADs) and thyroid dysfunction using a Mendelian randomization (MR) approach. Methods: Genetic predictors of hypothyroidism and hyperthyroidism were collected through the UK Biobank, including 337 159 individuals and 10 894 596 single nucleotide polymorphisms (SNPs). Genetic predictors of 6 ADs including systemic lupus erythematosus (SLE), ankylosing spondylitis (AS), type 1 diabetes mellitus (T1DM), rheumatoid arthritis (RA), primary biliary cholangitis (PBC), and multiple sclerosis (MS) were collected through the GWAS Catalog database, including 14 267 individuals and 7 071 163 SNPs, 22 647 individuals and 99 962 SNPs, 24 840 individuals and 12 783 129 SNPs, 58 284 individuals and 13 108 512 SNPs, 13 239 individuals and 1 124 241 SNPs, and 38 589 individuals and 156 632 SNPs. MR analysis was performed using the inverse-variance weighted (IVW) method. The horizontal pleiotropy was assessed using the MR-Egger regression, and sensitivity analysis was conducted with the leave-one-out. Results: IVW results showed that a higher risk of hypothyroidism was associated with T1DM (OR=1.007, 95%CI: 1.003-1.011, P<0.05), SLE (OR=1.005, 95%CI: 1.002-1.009, P<0.05), and RA (OR=1.013, 95%CI: 1.009-1.016, P<0.05); a higher risk of hyperthyroidism was associated with T1DM (OR=1.002, 95%CI: 1.001-1.003, P<0.05) and SLE (OR=1.002, 95%CI: 1.001-1.003, P<0.05). Conclusions Genetically predicted ADs are associated with an increased risk of thyroid dysfunction. A higher risk of hypothyroidism is associated with T1DM, SLE and RA; a higher risk of hyperthyroidism is associated with T1DM and SLE.