Objectives To test the validity of a novel protocol for 3D sagittal jaw discrepancy assessment (skeletal class determination) through comparison with common 2D indexes by the use of reduced FOV (10 × 10) CBCT which shows at least from the Frankfurt plane to the B point vertically, and from the most anterior between A and B point to Po point horizontally. Methods A sample of CBCT scans of 109 adult patients (46 females; 63 males; mean age 30 years ± 11.6) equally distributed between I, II and III class was selected. Skeletal class was evaluated with specific software using the distance of A and B point’s projection (AF-BF) on FHp (Frankfurt horizontal plane) and compared to 2D common indexes (ANB andWitts appraisal). The validity and reliability of the aforementioned analyses were determined using intra-class correlation coefficients, quadratic weighted Cohen’s K and sensitivity. Result A selected range of values of 2.5 ± 2.5 AF-BF showed a solid correlation with the ANB angle (r = 0.846, K = 0.838, p < 0.001) and moderate with Wits appraisal (r = 0.723, K = 0.720, p < 0.001). Conclusions AF-BF showed high reliability in skeletal class determination on reduced FOV CBCT without the use of S and N cephalometric landmarks.