There are no cone-beam computed tomography (CBCT)-based data on the anatomy of mandibular second molars in an Australian population. This study investigated the prevalence and descending morphology of mandibular second molars with and without C-shaped canals using retrospective analysis of CBCT scans. Scans from 715 patients were screened for the presence of C-shaped canals and assessed for cross-sectional configuration at five axial levels. Non-C-shaped molars were assessed for other morphological characteristics. Data were modelled against patient, tooth and CBCT scan characteristics. A total of 1278 teeth from 657 patients were evaluated. The overall prevalence of C-shaped canals was 13%. Cross-sectional configuration of C-shaped canals was variable, with an average of 2.8 unique cross-sections per tooth. Non-C-shaped teeth were predominantly Vertucci Type II (60%) and Type IV (29%) configurations in mesial roots, and Type I (91%) in distal roots. Additional roots occurred in 4.3% of teeth and there was a significant association between radix paramolaris and distal root bifurcation (P < 0.001). Cross-sectional analysis confirmed the complexity and variability of C-shaped canals. Clinicians should be cognizant of the prevalence and variability of C-shaped root canal morphology and how this may affect endodontic treatment.