Objective To assess the efficacy and safety of mytomycin C versus 5-fluorouracil for trabeculectomy. Methods We electronically searched the Cochrane Central Register of Controlled Trials (Issue 3, 2008), MEDLINE (1966 to October 2008), EMbase (1947 to October 2008), CMBdisk (1979 to October 2008).We also handsearched relevant conference proceedings. Data were extracted by two reviewers independently using an extraction form. The Cochrane Collaboration’ s RevMan 5.0 software was used for statistical analyses. Results Nine randomized controlled trials (RCTs) involving 482 participants (495eyes) were identified. The trials enrolled three types of participants (high risk of failure, moderate risk of failure, low risk of failure). As for high risk of failure, compared with mytomycin C, 5-fluorouracil appeared to increase the rate of postoperative complications (RR –5.74, 95%CI –9.91, –1.58). No significant differences were found in postoperative mean intraocular pressure(IOP) (WMD –?2.31, 95%CI –?7.34, 2.71), success rate (RR 1.13, 95%CI 0.91, 1.39) and visual acuity ≥3-line decrease (RR 1.46, 95%CI 0.43, 4.94). As for low risk of failure, there were no significant differences in success rate (RR 1.10, 95%CI 0.99, 1.22) and postoperative complications (RR 1.00, 95%CI –6.21, 8.21). Conclusion In both groups of high risk and low risk of failure, there are no significant differences in postoperative mean IOP and success rate. However, in the group of high risk of failure, compared with 5-fluorouracil, mytomycin C appears to raise the rate of postoperative complications; the rate of reducing the eyes pressure cannot be concluded based on current evidence. However, as the number of the studied cases is rather small and the period of observation is also limited, long-term follow-up of multi-central RCTs with a larger number of cases are still needed before definite conclusions can be made. Further studies are also needed to better determine the pharmacokinetics and cost-effective analyses involving the use of the two agents for glaucoma filtering surgery.