Abstract： Objective To evaluate the efficacy of mineral trioxide aggregate (MTA) and glass ionomer cement (GIC) for repair of furcation perforation.Methods Between January 2010 and December 2011,98 teeth with furcation perforation confirmed in Affiliated Guanghua Hospital of Sun Yat-sen University were randomly allocated to be subjected to repairing procedures in which MTA or GIC was applied.Follow-up assessments was performed at week 1 and months 1,3,6 and 12.Results MTA and GIC achieved a successful rate of 95.8％and 91.3％ in patients without root furcating lesion (P＞0.05).These figures were 92.0％ and 53.8％ for MTA and GIC in patients with root furcating lesion,respectively (P＜0.05).Conclusions MTA and GIC effectively facilitate the repair of furcation perforation without root furcating lesion.MTA is more effective for the treatment of furcation perforation in patients with root furcating lesion.