Objective:The purpose of this study was to investigate Morse taper implant–abutment joints by chemical, mechanical, and microscopic analysis.Materials and Methods:Surfaces of 10 Morse taper implants and the correlated abutments were inspected by field emission gun-scanning electron microscopy (FEG-SEM) before connection. The implant–abutment connections were tightened at 32 Ncm. For microgap evaluation by FEG-SEM, the systems were embedded in epoxy resin and cross-sectioned at a perpendicular plane of the implant–abutment joint. Furthermore, nanoindentation tests and chemical analysis were performed at the implant–abutment joints.Statistics:Results were statistically analyzed via one-way analysis of variance, with a significance level of P < 0.05.Results:Defects were noticed on different areas of the abutment surfaces. The minimum and maximum size of microgaps ranged from 0.5 μm up to 5.6 μm. Furthermore, defects were detected throughout the implant–abutment joint that can, ultimately, affect the microgap size after connection. Nanoindentation tests revealed a higher hardness (4.2 ± 0.4 GPa) for abutment composed of Ti6Al4V alloy when compared to implant composed of commercially pure Grade 4 titanium (3.2 ± 0.4 GPa).Conclusions:Surface defects produced during the machining of both implants and abutments can increase the size of microgaps and promote a misfit of implant–abutment joints. In addition, the mismatch in mechanical properties between abutment and implant can promote the wear of surfaces, affecting the size of microgaps and consequently the performance of the joints during mastication.