The aim of this study was to evaluate the biomechanical effect of rapid maxillary expansion (RME) on the craniofacial complex by using a three-dimensional finite element model (FEM) of the craniofacial skeleton. The construction of the three-dimensional FEM was based on computer tomography (CT) scans of the skull of a 12-year-old male subject. The CT pictures were digitized and converted to the finite element model by means of a procedure developed for the present study. The final mesh consisted of 2270 thick shell elements with 2120 nodes. The mechanical response in terms of displacement and von Mises stresses was determined by expanding the maxilla up to 5 mm on both sides. Viewed occlusally, the two halves of the maxilla were separated almost in a parallel manner during 1-, 3-, and 5-mm expansions. The greatest widening was observed in the dento-alveolar areas, and gradually decreased through the superior structures. The width of the nasal cavity at the floor of the nose increased markedly. However, the postero-superior part of the nasal cavity was moved slightly medially. No displacement was observed in the parietal, frontal and occipital bones. High stress levels were observed in the canine and molar regions of the maxilla, lateral wall of the inferior nasal cavity, zygomatic and nasal bones, with the highest stress concentration at the pterygoid plates of the sphenoid bone in the region close to the cranial base.