The objective of this study was to report the clinical evaluation results and 3-dimensional (3-D) dental and craniofacial characteristics observed in 2 male patients with mucopolysaccharidosis type II. The patients were evaluated clinically (soft tissue evaluation, evaluation of occlusion, periodontal and dental examinations) and by using craniofacial computed tomography, with evaluation of 3-D images in ITK-Snap v. 2.2 (Penn Image Computing and Science Laboratory, Philadelphia, PA; http://www.itksnap.org/) and 3-D Slicer (http://www.slicer.org/) software. Mandibular 3-D volumetric label maps were built from computed tomography scans of both patients and compared through superimposition on a healthy patient's mandibular images. Clinically, the patients presented the following oral manifestations: macroglossia, total open bite and generalized diastemas, and absence of caries. Patient 1 showed dental calculus and bleeding at the gingival margin. Patient 2 showed bleeding at the gingival margin, a permanent maxillary left central incisor missing as a result of trauma, and impacted permanent mandibular left and right second molars. 3-D images showed wide arches, prominent antegonial notches, a narrow mandibular body in the region of the antegonial notches, bilateral severe condylar hypoplasia, and enlarged coronoid processes. 3-D imaging and superimpositions revealed oral and skeletal displacements, contributing to the identification of changes in the course of mucopolysaccharidosis type II in patients with a late diagnosis.