Introduction: The aim of this study was to identify the root and canal morphology of maxillary first and second molars in Iranian population by taking and analyzing cone-beam computed tomography (CBCT) scans. Methods and Materials: Extracted maxillary first (n=125) and second (n=125) molars were collected from native Iranians and scanned by using a CBCT scanner. The number of roots and configuration of root canal system were classified according to Vertucci’s classification. Results: Two (1.6%) maxillary first and two (1.6%) maxillary second molars had four roots. Prevalence of root fusion was 2.4% and 8.8% in maxillary first and second molars, respectively. The most common canal morphology in the mesiobuccal roots of three-rooted first and second molars was Type I (46.4% and 80.8%, respectively), followed by Type VI (17.6%) in first molars. The predominant morphology of distobuccal and palatal roots in first and second molars was Type I. Additional canal types were also identified. Conclusion: Profound knowledge of anatomic variations is necessary prior to cleaning and obturation of the root canal system. The most common discovered root morphology was three separate roots in both tooth types. The greatest variation in canal anatomy was discovered in the MB canals of both the first and second molars.