The aim of this study was to investigate the root canal morphology of lower second molars in the Croatian subpopulation of the Zagreb region using cone-beam computed tomography (CBCT). We analyzed 3212 CBCT scans from the two radiology centers in Zagreb. The number of roots and root canals, the occurrence of C-shaped canals and additional roots were recorded. “C”-shaped roots were classified according to Melton classification. Canals in the mesial root were classified according to Vertucci. Lower second molars were found on 608 CBCT scans from a total number of 859. Among them, 78 (9.1%) had a “C”-shaped form. In the mesial roots, the frequencies of Vertucci types were: Type I in ninety-four cases (12.0%), Type II in three hundred and twenty cases (41.0%), Type III in six cases (0.8%), Type IV in three hundred and fifty-two cases (45.1%), Type V in three cases (0.4%), Type VI was found in four cases (0.5%) and Type VIII was found in one case (0.1%). Radix entomolaris and paramolaris were found in 29 (3.4%) lower second molars. The lower second molars in the Zagreb population show significant diversity in internal anatomy with a relatively high prevalence of “C”-shaped root canals and merged root canals in the mesial root.