Background. Pterygomaxillary dysjunction is the most dangerous part of Le Fort I osteotomy. Preoperative evaluation of the patient's anatomy in 3D imaging software may help to choose an appropriate surgical approach and minimize the risk of the operation. Objectives. The aim of this study was to evaluate the reproducibility of linear measurements performed at the pterygomaxillary junction using open source software. Material and Methods. The study population consisted of 101 patients who underwent a CBCT examination for reasons independent of this study. Eight anatomical landmarks in the pterygomaxillary junction were pre-defined to measure the thickness and length of this structure. Linear measurements between the landmarks were performed in duplicate by two independent observers over 14 days. The data was evaluated using Netfabb Basic Studio (Netfabb Company, Parsberg, Germany). An analysis of variance (ANOVA) studied the influence of certain factors (side, observer, and repetition) on the accuracy of the measurements. Results. The mean value of all the valid measurements was 2.76 mm for thickness and 16.71 mm for the length of the pterygomaxillary junction. ANOVA showed no inter-observer bias. None of the observers reported statistically significantly higher or lower values than the other observer (p > 0.05). The intra-observer reproducibility was better than the inter-observer reproducibility of the measurements. The intra-and inter-observer reproducibility analyzed for log-transformed absolute values of differences between the measurements was very good (< 0.5 mm mean difference for linear values reconstructed from the log). The results were from a relatively large population and offered useful and reproducible measurements using open source software during the planning of orthognathic procedures. Conclusions. The results confirmed the reproducibility of the measurements. This method may be used during the diagnostics and planning of Le Fort I osteotomy. We also propose further evaluation of open-source software programs. Their comparison may help standardize the planning of orthognathic procedures (Dent. Med. Probl. 2016, 53, 3, 320-331).