Objective The purpose of this study was to identify the variation of bi-dimensional cephalometric measurements following real head rotation. Material and methods Thirty cone beam-computed tomography (CBCT) head films were oriented according to three axes: horizontal Frankfort plane, transverse bi-orbital plane, and Opisthion-Nasion median plane. Axial rotation of 2 degrees, 4 degrees, 6 degrees, and 8 degrees from the Odontoidale point were performed. Horizontal and vertical linear and angular measurements were studied on lateral cephalograms derived from each rotation T0, T2, T4, T6, and T8. A paired t-test was applied to compare the measurements between T0 and each rotational angle. Results Of the 18 measurements, 55% showed statistically significant differences (P < 0.05) and 22% showed clinically significant differences, mostly at T6 and T8. Horizontal linear measurements Ba-A and N-Ba decreased, and vertical linear measurement G-Sn increased gradually, as the angle of head rotation increased. Angular measurements studied did not vary. Conclusions Head malpositions during X-ray acquisition should be avoided and rotated lateral CBCT cephalograms should be corrected and recentered to prevent any variation in linear measurements.