Objectives The aim of the present study is to identify the prevalence of radix entomolaris in mandibular first and second molars and to determine morphological classifications and associations with other root and canals. Methods Mandibular first and second molar teeth of 850 Turkish patients were evaluated using cone-beam computed tomography. A total of 2800 mandibular first molars and second molars were screened. The CBCT examination was performed at five different axial levels. The prevalence of total radix entomolaris, unilateral-bilateral, right-left side and gender distributions, and the classification of radix entomolaris's canal configurations were measured. Results Radix entomolaris was found in 2.9% (n = 25) of the patients and 1.2% (n = 34) of the teeth. The prevalence of radix entomolaris in mandibular first molars was higher than in mandibular second molars (p < 0.01), in males than in females (p < 0.05) and in right side than left side. An additional tubercle was found in 23% of the teeth with radix entomolaris. For buccolingual orientation, Type A canal variation was the highest and Type C canal variation was the lowest. Regarding locations of cervical parts, Type III canal variation was the highest while Type I canal variation was the lowest. Conclusions The prevalence of radix entomolaris was lower in the Turkish population than in other Asian populations but, in multiethnic societies, it needs attention. Before starting endodontic treatment, the clinician should examine the radiography thoroughly and apply advanced radiography methods when necessary. Cone-beam computed tomography is a valuable advanced radiography method for assessing such anatomical variations in vivo.