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Previous studies on the relationship between systemic lupus erythematosus (SLE) and autoimmune liver diseases (AILDs) are inconclusive. Therefore, we employed Mendelian randomization (MR) to explore the causal associations between SLE and AILDs. A two-sample MR analysis was performed using summary-level statistics sourced from genome-wide association study (GWAS) datasets. Inverse-variance weighting (IVW), MR‒Egger, and weighted median (WM) were further supported by several sensitivity analyses. We detected causal genetic associations between SLE and primary biliary cholangitis (PBC) (odds ratio (OR) = 1.31, 95% CI = 1.15–1.51, P < 0.01; adjusted OR = 1.63, 95% CI = 1.39–1.90, P < 0.01) and between SLE and primary sclerosing cholangitis (PSC) (OR = 1.09, 95% CI = 1.01–1.08, P = 0.03; adjusted OR = 1.10, 95% CI = 1.00–1.21, P = 0.04). No causal association was found between SLE and autoimmune hepatitis. We are the first to use MR analysis to explore the causal relationships between SLE and various AILDs, revealing an increased risk of PBC and PSC in individuals with SLE. • Previous studies have shown that the coexistence of AILDs in patients with SLE is common, indicating a potential causal relationship between these two conditions; however, that relationship is still unclear. • This is the first study to identify the causal effects of SLE on AILDs using two-sample Mendelian randomization analysis. • Our results may provide new evidence for diagnostic and therapeutic strategies in clinical practice. [ABSTRACT FROM AUTHOR]