Purpose: The aim of this study was to evaluate the effects of a variety of implant cleaning instruments on different implant surfaces, specifically surface roughness and cleaning efficacy. Materials and Methods: Biofilm layers of Streptococcus mutans were cultivated on titanium disks with four different surface structures (polished, grit-blasted, acid-etched, and acid-etched/grit-blasted). Five disks each were cleaned using nine mechanical implant cleaning instruments or an erbium:yttrium-aluminum-garnet laser. Surface roughness (average, Ra; maximum, Rz) and waviness (Lr) were evaluated by two-dimensional laser profilometry. Surface structure damage and cleaning scores were assessed by scanning electron microscopy. Statistical analyses of the results were performed with one- and two-way analyses of variance and Bonferroni-Dunn multiple-comparison post hoc analysis (α = .05). Results: Ra and Rz values for the acid-etched surfaces and Ra, Rz, and Lr values for the polished and the grit-blasted surfaces showed no significant differences between the different cleaning methods or cleaning instruments compared to the control (not cultured, not cleaned) groups. Significantly lower Ra and Rz values on grit-blasted/acid-etched implant surfaces were found following use of the Sonic-Flex clean with prophylaxis brush and the plastic curette compared to Satelec ProphyMax with Periosoft curette. Ra and Rz values of the different implant structure surfaces before cleaning were significantly different between all implant surfaces except for the polished compared to the acid-etched surfaces. Conclusions: Cleaning effect and alterations of the implant surfaces were strongly dependent on the implant cleaning method used. Keywords: cleaning instruments, implant surfaces, laser profilometry, scanning electron microscopy, surface roughness