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Objective To identify and compare the morphology and dimensions of the nasopalatine canal (NPC) of individuals with and without cleft lip and palate using Conical Beam Computed Tomography (CBCT) images and to relate the results to the type of cleft and tooth absences in the region. Setting This is a cross-sectional, analytical study with a retrospective sample. Patients, Participants 100 CBCT exams from patients with cleft lip and palate and 100 CBCT exams from patients without cleft lip and palate were used. Interventions The NPC was evaluated for its morphology and measurements in the coronal, sagittal, and axial reformatting of CBCT exams. Results It was obtained as a result that in the group of patients with a cleft, the shapes of funnel, banana, and needle of the NPC were more frequent than in the control group. Patients with cleft lip and palate had significantly a larger nasopalatine foramen and a larger NPC diameter, besides a significantly shorter NPC, compared to controls. In both groups, edentulous patients had less anterior maxillary bone thickness, when compared to patients with maxillary anterior teeth. Patients with clefts had a bone thickness buccal to the NPC less than in the control group. Conclusions This study confirms the anatomical variability of NPC in patients with cleft lip and palate. This finding reinforces the need for thorough surgical planning of the anterior region of the maxilla, in CBCT exams, by the dentist.