Objective: This study aimed to compare cranial base linear and angular measurements between individuals with skeletal open bite and different sagittal skeletal relationships. Materials and methods: This observational and cross-sectional study included 101 lateral radiographs of young Latin-American individuals with skeletal open bite that met the inclusion criteria and were collected from a private radiological centre. Three groups were formed. Groups 1, 2 and 3 included individuals with skeletal open bite (negative overbite and FMA > 30°) and Class I (n = 31), II (n = 35) and III (n = 35) sagittal skeletal relationship, respectively. The anterior and posterior cranial bases (SN and SBa), and cranial base angles (BaSN and ArSN) were measured. Groups were compared with one-way analysis of variance and post-hoc Scheffé tests. The influence of predictor variables on the cranial base were evaluated with linear regressions (α = 0.05). Results: The cranial base angles were significantly smaller (approximately 3° to 5°) in the skeletal open bite Class III group (BaSN = 127.97°± 5.86°, ArSN = 120.19°±6.12°) when compared with the other groups. BaSN angle, Class I versus Class III (p < 0.001) and Class II versus Class III (p < 0.001). ArSN angle, Class I versus Class III (p = 0.005) and Class II versus Class III (p = 0.026). Multiple linear regressions showed that sex had a significant influence on both cranial base dimensions with men showing larger values than women. Conclusions: Skeletal open bite Class III individuals show a smaller cranial base angle than Skeletal open bite Class I or II individuals.