To address the following focused question: What is the quality of reporting of pre-clinical research for the study and treatment of mucositis/peri-implantitis? Electronic databases of the PubMed and the Cochrane Library were searched for animal studies reporting on pathogenesis or therapy of either peri-implant mucositits or peri-implantitis and completed by dual manual searches in duplicate between 1992 and May 2011. Quality assessment (i.e. grading of a checklist of 20 items in different categories) of selected full-text articles was performed according to the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines. Following screening, 75 publications were eligible for the review. For publications reporting on pathogenesis (n = 7) and therapy (n = 1) of peri-implant mucositis, minimum gradings were assigned to items 5 (Methods/Ethical Statement), 9 (Methods/Housing and husbandry), 11 (Methods/Allocation animals to experimental groups), 14 (Results/Baseline data), and 17 (Results/Adverse events). For publications reporting on pathogenesis (n = 34) and therapy (n = 33) of peri-implantitis, minimum grades were mainly assigned to items 9, 11, 14, and 17. This systematic review has identified missing information in the publications on pre-clinical research for the study and treatment of mucositis/peri-implantitis. © 2012 John Wiley & Sons A/S.