The aim of this study was to verify the existence of variations of the skull base morphometry between patients with cleft lip and palate, with dentofacial deformity group and without dentofacial deformity (control group). Methodology: Three groups of patients, one group with dentofacial deformity associated without cleft lip and palate (DFSF), another with cleft lip and palate (FS), and another group of patients without cleft and without deformity (CTRL) were included by means of medical records and DICOM (Digital Imaging Communications in Medicine) images of their CT (Computed Tomography) scans. By identifying the basio (Ba), sela (S) and nasio (N) cephalometric points in the Dolphin Imaging 11.9 software, the distance between the points Ba-S (DBaS), S-N(DSN) and the angle formed between points Ba-S-N (AnGBaSN) were the variables. They were statistically evaluated by means of the p> 0.05. Results: Twenty patients were included on each group. We found that the distance S-N (DSN) is not statistically different between the groups, but the Ba-S distance (DBaS) and the Ba-S-N angle (AnGBaSN) are statistically different when compared the three groups. The Ba-S-N angle (AnGBaSN) did not present statistically different when compared to the control group (CTRL) and the group cleft lip and palate patients (FS), but presented statistical difference in relation to the group of patients with facial deformities without cleft lip and palate (DFSF). The distance BaS (DBaS) presented statistical difference between the group of patients with fissures (FS) in relation to the other two groups. Conclusion: Differences in skull base morphometry among patients with dentofacial deformity associated or not with cleft lip and palate suggest that standardized values for cephalometric analyzes involving such structures should be used with caution. New cephalometric patterns, especially by 3D analysis, are desirable to compensate for these anatomical differences.