Mineral trioxide aggregate (MTA) has been widely used to repair various kinds of tooth perforations, but its use for obturation of the entire root canal has not been reported. We report two cases of tooth perforation successfully repaired with MTA. The first patient was a 78-year-old male with calcified canal and pulp floor perforation in the left maxillary first premolar. After bypass of the calcified palatal canal, both buccal and palatal canals were filled with gutta percha, and the pulp floor perforation was repaired with MTA. Clinical success with no evident radicular lesion was found at the 18-month follow-up. The second patient was a 51-year-old female with a stripping perforation in a C-shaped root canal of the right mandibular second molar detected after removal of a post. Following root canal debridement and calcium hydroxide therapy to control inflammation at the stripping perforation site, apical and furcation bone healing were observed by radiographic examination. The stripping perforation was repaired by obturation of the entire C-shaped root canal with MTA. Observation at the 9-month follow-up revealed bone healing without any clinical symptoms and signs. These cases suggest that MTA is an alternative root canal obturation material for treatment of stripping perforation in a C-shaped root canal and for repair of pulp floor perforation.