The association between cranial base morphology and Class Ⅱ malocclusion is still not fully understood. The purpose of this study was to investigate the morphological characteristics of the cranial base in children with Class Ⅱ malocclusion. Lateral cephalograms of 100 children with Class Ⅱ malocclusion were compared with their counterparts of 100 subjects with normal occlusion. Ten landmarks on the cranial base were identified and digitized. Cephalometric analysis utilizing 7 angular and 18 linear measurements were undertaken. Multivariate Hotelling's T^2 tests indicated that statistical differences existed between Class Ⅱ groups and normal controls in boys. Nevertheless, there was no significant difference between the two groups in girls. It is concluded that there are longer anterior cranial base and larger cranial base angle in children with Class Ⅱ malocclusion. The association between cranial base morphology and other types of malocclusion needs clarification. Further study with geometric morphometric analysis is warranted.