Objective To evaluate the curative effectiveness and safety of transanal endoscopic microsurgery (TEM) vs. radical surgery (RS) for the patients with rectal malignant tumor, and to provide information for clinical research and practice. Methods Through computer searching The Cochrane Central Register of Controlled Trials, PubMed, OVID, CBM and CNKI from inception to April 2010, and hand searching relevant journals including Chinese Journal of Surgery and Chinese Journal of Evidence-Based Medicine, the randomized controlled trails (RCTs) and non-randomized controlled trails (NRCTs) comparing TEM with RS for rectal malignant tumor were collected. Data were extracted and evaluated by two reviewers independently according to the Cochrane Handbook for Systematic Reviews. Meta-analyses were conducted using the Cochrane collaboration’s software RevMan 5.0. Results One RCT and four NRCTs met the selection criteria, involving 929 patients. The methodological quality of all trials was low with possibility of bias. The meta-analyses showed that: a) Three studies reported local recurrence in T1 stage patients. There was a significant difference in local recurrence between the two groups (OR=12.61, 95%CI 2.59 to 61.29, P=0.002); b) Two studies reported disease-free survival in T1 stage patients. There was no significant difference between the two groups in disease-free survival (OR=1.12, 95%CI 0.31 to 4.12, P=0.86); c) Three studies reported overall survival in T1 stage patients. There was no significant difference between the two groups (OR=1.09, 95%CI 0.57 to 2.08, P=0.80); and d) Three studies reported postoperative complications in T1 stage patients. There was a significant difference between the two groups in terms of complications (OR=0.05, 95%CI 0.02 to 0.10, Plt;0.00001). Conclusion For T1 stage patients, TEM is associated with less injury of tissue, less operative bleeding, short duration of hospital stay, and low incidence of postoperative complications. The disease-free and overall survivals are comparable to those of RS, but the local recurrence rate is higher. The role of TEM in T2 stage patients is still under discussion. However, the trails available for this systematic review are of lower methodological quality, and bias may exist due to NRCTs. Therefore, more high quality RCTs are required.