INTRODUCTION: Complex root canal systems appear regularly on fused roots. The aim of this observational study was to evaluate the prevalence of fused roots and root canal merging in the first and second upper and lower permanent molars by using cone-beam computed tomography technology. METHODS: A large sample of cone-beam computed tomography examinations was accessed. Maxillary and mandibular molars were classified according to number of roots, root fusions, types of root canal system configurations, merging positions, and merging levels. The Z test for proportions was used to analyze the differences in independent groups. A value of P < .05 was considered significant. RESULTS: This study included 4120 molars. The prevalence of root fusions was 7.1% and 25.2% for the first and second upper molars, respectively; for the first and second lower molars, the prevalence was 0.7% and 12.6%, respectively. In addition, 8.6% and 10.1% of the second upper and lower molars, respectively, had fused roots with canal merging; moreover, 7.1% and 2.1% of the second upper and lower molars had single or 2 non-merging root canals, respectively. The most usual merging position for the first upper molars is between the distobuccal root and palatal root canals; for the second upper molars, the most usual merging position is between the mesiobuccal root and distobuccal root canals. Merging appears more commonly at the apical level. Significant differences were found between the teeth and gender groups. CONCLUSIONS: When approaching the second upper and lower molars, the clinician should be aware of uncommon morphologies. In our sample, 15.7% and 12.2% of the second upper and lower molars, respectively, had fused roots, which did not present the usual configurations with independent root canals.