Titanium or zirconium computer-aided design/computer-aided manufacturing abutments are now widely used for aesthetic implant treatments; however, information regarding microscopic structural differences that may influence the biological and mechanical outcomes of different implant systems is limited. Therefore, the characteristics of different connection systems were investigated. Optical microscopic observation and scanning electron microscopy showed different characteristics of two internal systems, namely the Astra Tech and the Replace Select system, and for different materials. The scanning electron microscopic observation showed for the Astra Tech that the implant-abutment interface seemed to be completely sealed for both titanium and zirconium abutments, both horizontally and sagittally; however, the first implant-abutment contact was below the fixture top, creating a microgap, and fixtures connected with titanium abutments showed significantly larger values (23·56μm±5·44 in width, and 168·78μm±30·39 in depth, P<0·001). For Replace Select, scanning electron microscopy in the sagittal direction showed that the sealing of titanium and zirconium abutments differed. The seal between the implant-titanium and implant-zirconium abutments seemed to be complete at the butt-joint interface; however, the displacement of the abutment in relation to the fixture in the lateral direction was evident for both abutments with no statistical differences (P>0·70), creating an inverted microgap. Thus, microscopy evaluation of two commonly used internal systems connected to titanium or zirconium abutments showed that the implant-abutment interface was perfectly sealed under no-loading conditions. However, an inverted microgap was seen in both systems, which may result in bacterial accumulation as well as alteration of stress distribution at the implant-abutment interface.