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Purpose: This study aimed to comparatively evaluate the stress distribution of bones surrounding the implant system to which both titanium and polyetheretherketone (PEEK) abutments are applied using a three-dimensional finite element analysis. Methods: The three-dimensional implant system was designed by the computer-aided design program (CATIA; Dassault Systemes). The discretization process for setting nodes and elements was conducted using the HyperMesh program (Altair), after finishing the design of each structure for the customized abutment implant system. The results of the stress analysis were drawn from the Abaqus program (Dassault Systèmes). This study applied 200 N of vertical load and 100 N of oblique load to the occlusal surface of a mandibular first molar. Results: Under external load application, the PEEK-modeled dental implant showed the highest von Mises stress (VMS). The lowest VMS was observed in the Ti-modeled abutment screws. In all groups, the VMS was observed in the crestal regions or necks of implants. Conclusion: The bones surrounding the implant system to which the PEEK abutment was applied, such as the cortical and trabecular bones, showed stress distribution similar to that of the titanium implant system. This finding suggests that the difference in the abutment materials had no effect on the stress distribution of the bones surrounding implants. However, the PEEK abutments require mechanical and physical properties improved for clinical application, and the clinical application is thought to be limited.