OBJECTIVE: To investigate the safety of thalidomide in the treatment of immune-related bowel diseases for providing clinical reference. METHODS: Thirty-five patients with immune-related bowel diseases (31 Crohn's disease, 2 ulcerative colitis and 2 Behcet's disease) treated with thalidomide were enrolled in this study. The incidence, type, severity, duration of thalidomide related adverse drug reaction (ADR) and the dose-effect relationship of neurotoxicity were analyzed. RESULTS: All the patients were treated with a mean dose of thalidomide (109.29 +/- 30.37) mg/d for (18.8 +/- 12.4) months, and 33 occurred ADR. The three most frequent ADR were numbness [51.4% (18/35) ], somnolence [48.6% (17/35) ] and dermatitis [37.1% (13/35) ]. The median time to development of these three ADR were 6.50, 0.25, and 1.00 months, respectively. Severe ADR leading to withdrawal accounted for 20.0% (7/35), including reasons of peripheral neuritis (3/7), dermatitis (2/7) and myelosuppression (2/7). The incidence of peripheral neuritis was not significantly related to the maximal and initial dose of thalidomide (P > 0.05). CONCLUSIONS: Although the incidence of ADR was relatively high during the treatment of thalidomide, most of them were mild and well tolerated. Thalidomide can be safely used in patients with immune-related bowel diseases under close monitoring.