[Abstract] Objective To assess the efficacy and safety of thalidomide in patients with acquired immune deficiency syndrome(AIDS)-related recurrent aphthous ulcer(RAU). Methods After identifying the study question of the efficacy and safety of thalidomide in patients with AIDS-related RAU, we searched Cochrane Controlled Trials Register, Medline, EMBASE, CBM, CNKI, VIP till September 2011. Risk of bias assessment with Cochrane Collaboration’s tool, and data extraction of included studies were conducted by two reviewers in duplicate. The software RevMan 5.0 was used for analysis. Results Two randomized controlled trials were included. Meta-analysis showed: The rate of complete healing of ulcers in thalidomide group was significantly higher than the placebo group, and the difference was statistically significant; In adverse reactions, the incidence of rash and somnolence in thalidomide group was higher than the placebo group, but there was no difference of peripheral sensory neuropathy in both groups. Conclusion Thalidomide treatment of AIDS-related RAU was superior to placebo, in the meantime increased the incidence of adverse reactions. Further high-quality and large-scale as well as multicenter randomized controlled trials are still needed to evaluate the efficacy and safety of thalidomide in patients with AIDS-related RAU.