Objective: The purpose of this study was to compare the precision and accuracy of linear measurements for Le Fort I osteotomy performed by two different imaging software programs and obtained from three-dimensional cone beam CT (3D-CBCT) images. Methods: The study population consisted of 11 dried skulls submitted to CBCT, which generated 3D images. Linear measurements were based on craniometric anatomical landmarks pre-defined by the authors as specifically used for Le Fort I osteotomy and were identified by two radiologists twice each, independently, using Vitrea 3.8.1 (Vital Images Inc., Plymouth, MN) and open-source digital imaging communication in medicine viewer OsiriX 1.2 64-bit (Pixmeo, Geneva, Switzerland). Subsequently, a third examiner made physical measurements using a digital caliper (167 series; Mitutoyo Sul Americana Ltd, Suzano, SP, Brazil). Results: The results demonstrated a statistically significant difference between OsiriX and the gold standard, especially in the pterygoid process (TPtg L 5 0.019, LLpPtg R 5 0.016 and LLpPtg L 5 0.012). Vitrea showed no statistical difference in comparison with the gold standard, and showed a high level of accuracy in all the measurements performed. The major difference found was 0.42 mm (LLpPtg R). Interexaminer analysis ranged from 0.90 to 0.97 using Vitrea and from 0.8 to 0.97 using OsiriX. Intraexaminer correlation coefficient ranged from 0.90 to 0.98 and from 0.84 to 0.98 for Examiners 1 and 2, respectively, using Vitrea and from 0.93 to 0.99 for Examiner 1 and from 0.64 to 0.96 for Examiner 2 using OsiriX. Conclusion: Vitrea may be considered as precise and accurate, insofar as it was able to perform all the 3D linear measurements. On the other hand, linear measurements performed using OsiriX were not successful in producing accurate linear measurements for Le Fort I osteotomy.