We hypothesized that variations from normal craniofacial anatomy in Class II and Class III malocclusions are associated with 2 unreported or non-emphasized features that vary during growth: position of sella turcica and palatal plane inclination. Objective: to compare morphological characteristics between Class III and Class II malocclusions, specifically the cants of the anterior cranial base (SN) and palate (PP) and their relations to occlusion. Method: Lateral cephalographs from 2 groups: Class III (age 10.09±1.87yrs; n=51, 35 boys-16 girls) and Class II, division 1 (age 9.9±1.43yrs; n=84, 41 boys-43 girls) were analyzed following a standardized method. Angular and linear measurements gauged relations within and between the cranial base, maxilla, and mandible, including SN and PP to the horizontal (SN/H, PP/H). Statistics comprised t-tests and analyses of variance for group differences, and the Pearson product moment correlation coefficient for associations between parameters. Results: SN was on average flatter (SN/H=6.7o±3.42o) than the norm (8o±2o) in Class III, but inclined posterior-inferiorly in Class II malocclusions (SN/H=13.25o±2.76o). Likewise, opposite inclinations were observed with PP/H, rotated upward-backward in Class III (3.88o±3.41o; norm: 0o±2o), and tipped down posteriorly (-6.38o±2.72o) in Class II patients. Statistically significant differences were noted for all measurements except ramus height, and gonial angle. When both groups were merged to evaluate deviations across opposite malocclusion poles, high correlations were noted between: SN/H and PP/H (r=-0.79), overjet and PP/H (r=-0.82), overjet and SN/H (r=0.69). Conclusions: 1-the association between inclinations of palatal and cranial bases and overjet/crossbite suggests an adaptive mechanism between teeth and cranial base, seemingly through the maxilla. In Class III, a sustained anterior crossbite generates forces against the maxilla causing retrognathism that otherwise may not exist. 2-the important role maxillary-mandibular adaptations play during the development of both malocclusions would favor early orthopedic treatment, but further research is needed to test this hypothesis.