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Purpose: The purpose of this study was to evaluate the clinical accuracy of the fusion of intra-oral scans in cone-beam computed tomography (CBCT) scans using two commercially available software packages., Materials and Methods: Ten dry human skulls were subjected to structured light scanning, CBCT scanning, and intra-oral scanning. Two commercially available software packages were used to perform fusion of the intra-oral scans in the CBCT scan to create an accurate virtual head model: IPS CaseDesigner® and OrthoAnalyzer™. The structured light scanner was used as a gold standard and was superimposed on the virtual head models, created by IPS CaseDesigner® and OrthoAnalyzer™, using an Iterative Closest Point algorithm. Differences between the positions of the intra-oral scans obtained with the software packages were recorded and expressed in six degrees of freedom as well as the inter- and intra-observer intra-class correlation coefficient., Results: The tested software packages, IPS CaseDesigner® and OrthoAnalyzer™, showed a high level of accuracy compared to the gold standard. The accuracy was calculated for all six degrees of freedom. It was noticeable that the accuracy in the cranial/caudal direction was the lowest for IPS CaseDesigner® and OrthoAnalyzer™ in both the maxilla and mandible. The inter- and intra-observer intra-class correlation coefficient showed a high level of agreement between the observers., Clinical Relevance: IPS CaseDesigner® and OrthoAnalyzer™ are reliable software packages providing an accurate fusion of the intra-oral scan in the CBCT. Both software packages can be used as an accurate fusion tool of the intra-oral scan in the CBCT which provides an accurate basis for 3D virtual planning.