To explore the prevalence and distribution pattern of the root variations of permanent mandibular first and second molars in an eastern Chinese population.Cone-beam computed tomography images were collected retrospectively from 261 Chinese patients in Suzhou Stomatological Hospital. The incidences of the root variations were determined. The trait frequency differences between genders and sides were tested using Chi-square test with SPSS 13.0 software program. Correlations in the occurrence of the root variations between antimeric teeth, as well as between the two types of molars were analyzed with Spearman rank correlation test.The incidence of three-rooted mandibular molars was 24.7% (108/437) counted by teeth, and 27.9% (56/201) counted by individuals. The incidence of the antimeric teeth in both sides was 66.1% (37/56) and the correlation coefficient was 0.738 (P0.01). The incidence of C-shaped rooted in mandibular second molars was 43.3% (180/416) counted by teeth, and 49.7%(96/193) counted by individuals. The bilateral incidence was 79.2% (76/96) and the correlation coefficient was 0.790 (P0.01). The incidence of the female group was significantly (P0.05) higher than males. No significant correlation was found between the occurrence of three-rooted mandibular first molars and group C-shaped toot in mandibular second molars (r=0.033, P0.05).The prevalence of three-rooted mandibular first molars and C-shaped root in mandibular second molars are high in the eastern Chinese population. Understanding their distribution patterns may be useful for clinical practice.