BACKGROUND: Dysregulation of immune system could be a vital stimulant of colorectal cancer development. However, there was lacking of a comprehensive and rigorously conducted meta-analysis on association between autoimmune diseases and risk of colorectal cancer. METHODS: Literature retrieval was performed based on PubMed, Web of Science, and Embase from inception to January 2025. Observational cohort studies reporting incidence or risk ratio of colorectal cancer among patients with autoimmune disorders as exposures were eligible. Newcastle-Ottawa Scale was utilized for quality appraisal. Incident cases per 100 000 person-years at risk were used for incidence analysis as secondary endpoint. Relative risk was the primary endpoint and therefore adjusted risk ratio or hazard ratio with 95% confidence interval were effect sizes. RESULTS: 523 studies were included, containing 91,265,886 participants. Most eligible studies were high (n = 327) and medium-quality (n = 193) in methodology. Incidence of colorectal cancer among general or specific autoimmune disease patients was higher than that of general population. Pooled risk ratio for overall analysis was 1.244 (95%CI 1.190-1.300, p<0.001). The results were consistent irrespective of sub-localization (colon: 1.308, p<0.001; rectum: 1.173, p<0.001), sex (male: 1.229, p<0.001; female: 1.209, p<0.001) and country (Nordic: 1.301, p<0.001; Western: 1.213, p<0.001; East Asian: 1.213, p<0.001). Specifically, primary sclerosing cholangitis, idiopathic inflammatory myopathies, inflammatory bowel disease, autoimmune hepatitis, ANCA-associated vasculitis, sarcoidosis, scleroderma, type 1 diabetes, psoriasis, membranous nephropathy, hidradenitis suppurativa and idiopathic thrombocytopenic purpura were associated with higher risk of colorectal cancer compared to disease-free counterparts. Interestingly, several autoimmune diseases might help to lower colorectal cancer risk, especially rheumatoid arthritis. CONCLUSIONS: Patients with autoimmune diseases were associated with significantly higher risk of colorectal cancer under generally or specific settings. Unlike our gastric and small bowel cancer pooled results, this risk-increasing impact on colorectal cancer was quite consistent across Nordic, Western and East Asian countries. Both digestive organ-specific or systemic autoimmune diseases could significantly increase risk of colorectal cancer. However, several autoimmune diseases might act as protective factors against colorectal cancer, especially rheumatoid arthritis, while it had no such effects on gastric or small bowel carcinogenesis.