Objective:To assess the therapeutic effects and adverse effects of mycophenolate mofetil(MMF)and cyclophosphamide(CTX)in the treatment of refractory nephrotic syndrome(RNS) in the systematic review of randomized controlled trials. Methods:We searched PubMed(1966~2009),EMBASE(1984~2009),CBM(1979~2009),CNKI(1994~2009),VIP(1984~2009),CMCC(1994~2009)and Wanfang database(1982~2009)with key words of “mycophenolate mofetil”,“cyclophosphamide” and “refractory nephrotic syndrome” to identify randomized controlled trials of mycophenolate mofetil versus cyclophosphamide for refractory nephrotic syndrome patients. The quality of literature was evaluated,and Meta-analysis was conducted using RevMan 4.2.9 software. Results:Eight RCTs were identified. There was no evidence showing a publication bias except hepatic lesion’s study after Begg’s test analysis. Compared with CTX groups,MMF increased the clinical remission rate,including complete remission rate and partial remission rate(P < 0.05). It also significantly reduced the adverse effects(P < 0.05). Conclusion:The therapy of MMF plus steroids were more effective than that of CTX plus steroids in clinical remission of RNS,and had fewer adverse effects.