The main purpose of this study was to investigate the root and canal morphology of Sri Lankan and Japanese permanent dentition. Two thousand Sri Lankan and 976 Japanese permanent teeth were examined. The number of roots in premolars and molars and the prevalence of C-shaped (gutter shaped) roots in mandibular second molars were recorded. Root canal morphology was studied using a clearing technique. The examination of root canal systems of the teeth was based on Vertucci’s classification. A higher prevalence of two-rooted maxillary first premolars was observed in Sri Lankans than in Japanese. Sri Lankan maxillary first and second premolars displayed a higher incidence of two canal and two apical foramina forms than those of Japanese. Canal morphology of mandibular first premolars showed higher occurrence of two canals with type V (1-2) canal configuration in Sri Lankans than in Japanese. In mandibular molars, Japanese presented with a higher incidence of three-rooted first molars and one-rooted second molars than Sri Lankans. C-shaped root was seen in 5.7% of Sri Lankan and 18.8% of Japanese second molars examined. In the distal root of mandibular first molars, Japanese showed a higher prevalence of two apical foramina with type IV (2) and additional canal forms than that of Sri Lankans. Japanese mandibular second molars exhibited a higher occurrence of one-root canal forms than that of Sri Lankans. In addition, mandibular incisors and canines of Sri Lankans showed a higher prevalence of two canals with type III (1-2-1) canal form than Japanese. Root and canal morphologies of Japanese and Sri Lankan people are consistent with those of people of East Asian and European (western Eurasia) origin, respectively. In human dentition, the differences of the internal canal morphology are more evident and constant than that of external root morphology among different population groups.