To validate the accuracy and reproducibility of linear measurements of three-dimensional (3D) images and to compare the measurements with the direct anthropometry method on cleft lip and palate (CLP) patients. Nineteen linear facial measurements were derived from 16 standardized surface landmarks obtained from 37 cleft patients (20 males, 17 females; mean age 23.84 years, standard deviation ± 6.02). They were taken manually with calipers and were compared with the digitally calculated distance on the 3D images captured using the VECTRA-M5 360° Imaging System with pre-marked landmarks. Another pair of 19 linear measurements were computed on the 3D images 2 weeks apart for intra- and inter-observer agreements. Statistical analyses used were paired t test, the Bland-Altman analysis, and the intra-class correlation coefficient (ICC) index. Most of the linear measurements showed no statistically significant differences between the proposed method and direct anthropometry linear measurements. Nevertheless, bias of the 3D imaging system is present in the linear measurements of the nose width and the upper vermillion height. The measurements' mean biases were within 2 mm, but the 95% limit of agreement was more than 2 mm. Intra- and inter-observer measurements generally showed good reproducibility. Four inter-observer measurements, the upper and lower face heights, nose width, and pronasale to left alar base were clinically significant. Measurements obtained from this 3D imaging system are valid and reproducible for evaluating CLP patients. The system is suitable to be used in a clinical setting for cleft patients. However, training of the operator is strictly advisable.