Background: Epidemiological observational studies investigating the association between cathepsins and autoimmune diseases have shown inconsistent results. Hence, we conducted a Mendelian randomization analysis to assess the potential causal impact of cathepsins on these diseases. Methods: Employing a two-sample Mendelian randomization analysis, we used single nucleotide polymorphisms as instrumental variables to examine the impact of cathepsins on autoimmune diseases. The research comprised univariable and multivariable Mendelian randomization analyses, focusing on individual and combined effects of cathepsins. Statistical techniques included inverse variance weighted method and supplementary methods like MR-Egger for comprehensive assessment. Results: In our Mendelian randomization study, we identified diverse associations between cathepsins and autoimmune diseases. Specifically, cathepsin G was found to significantly increase the risk of myasthenia gravis, while the effects of cathepsin B on rheumatoid arthritis and systemic lupus erythematosus varied. Furthermore, multivariable analysis revealed significant correlations between cathepsins F, G and Z with myasthenia gravis. Importantly, no evidence of reverse causation or horizontal pleiotropy was observed. Conclusion: The study establishes a significant causal relationship between cathepsin G and myasthenia gravis risk.