Purpose: The purpose of this study was to compare marginal fit of Zirconia and Polyetheretherketone (PEEK) inlay retained fixed partial dentures (IRFPD) fabricated by using a computer-aided design and computer-aided manufacturing (CAD-CAM) system. Materials and Methods: Sound Mandibular second premolar and mandibular second molar were selected to simulate a clinical situation of a missing mandibular first molar and embedded in an epoxy resin (master model). Both teeth received a standard preparation of IRFPD with respect to all-ceramic preparation design parameters. The master model was duplicated into 18 epoxy resin models for standardization during testing procedure, and 18 IRFPDs were fabricated with CAD-CAM system and divided into 2 groups according to materials type (n=9); Group 1: 3-mol yttria-stabilized tetragonal zirconia polycrystal (3Y-TZP), Group 2: PEEK. Marginal Discrepancy of all bridges was tested before and after cementation with RelyX U200 self-adhesive resin cement (SARC) by using an optical digital microscope with the aid of an image analysis system. Results: Significantly lower marginal gap values were obtained in Zirconia group before and after cementation in comparison to PEEK group. There was also a significant increase of marginal gap after cementation in both groups, with higher mean in Zirconia group. Conclusion: The margins of IRFPDs performed well with recommended bonding protocols for both materials and present a viable treatment option for replacing a missing single posterior tooth. Both materials presented clinically accepted results of marginal discrepancy less than 120 μm. Further studies simulating clinical conditions are needed to understand how they perform in function.