Introduction. One of the problems encounted in endodontic treatment is the treatment of vital open apex teeth. Among different materials used for this purpose, Calcium hydroxide is the most widly used material. The purpose of this study was to compare a newly introduced material called MTA (Mineral Trioxide Aggregate) with calcium hydroxide in apexogenesis procedure.Methods: Fourty open apex canine teeth of 10 young cats were used in this study. Crowns of the teeth were resected and access cavities were slightly extended. Floor of pulp chamber of 16 teeth were packed with MTA and that of the other 16 teeth with Ca(OH)2.Access cavities were double sealed using ZOE and Amalgam. After 4-6 months the animals were sacrificed and the pulp and periodical tissues were examined by histologic evaluation. Four intact teeth were also used as negative control and 4 teeth without coronal seal were used as positive control.Results. Radiographic evaluation of MTA treated teeth after six months indicated that the apex of all of the teeth were closed and no calcified bridge was observed. In contrast, the apex of 13 out of 16 teeth treated with Ca(OH)2 had been closed and in calcium hydroxide samples calcified bridge had been formed. Histologically, there was a significant difference in microscopic changes of the pulp between the two treatment groups (P<0.05). The pulp of the teeth with MTA was similar to that of a normal teeth and they showed no calcified bridge. Furthermore, histologic investigation of the periapical area showed no statistically significant difference between the two groups.Discussion: Based on the results obtained in this study and the previous findings despite the fact that Ca(OH)2 may result in the apical closure because MTA causes less pulpal changes in apexogenesis need MTA treated teeth may not further root canal therapy. Therefore, MTA application is superior to Ca(OH)2 for apexogenesis procedures.