The aims of the study were to investigate the incidence of C-shaped root canal systems in mandibular second molars in a native Chinese population using radiography and clinical examination under microscope and to compare the relative efficacies of these methods. For the recognition of C-shaped root canal system, 1 146 mandibular second molars were selected and examined. Teeth with C-shaped canal systems were categorized by using the radiographic classification criteria and the modified Melton's method. C-shaped canals were identified in 397 (34.64%) mandibular second molars by radiography (type I, 31.23%; type II, 38.29%; type III, 30.48%). Clinical examination showed that 449 (39.18%) cases exhibited C-shaped canal systems (C1, 22.94%; C2, 48.11%; C3a, 15.59%; C3b, 13.36%). As for the result of the radiographic and clinical combined examination, C-shaped root canals were found in 473 (41.27%) mandibular second molars (C1, 21.78%; C2, 45.67%; C3a, 16.70%; C3b, 15.86%). The incidence of C-shaped root canal diagnosed by radiographic method was statistically different from that by clinical examination and the combined examination (P,0.05). The study indicated a high incidence of C-shaped canal system in a Chinese population. The combination of microscopic and radiographic examination is an effective method in identifying the C-shaped root canal system.