Purpose: To qualitatively investigate the microbiologic profile in peri-implantitis by systematically reviewing the published literature on peri-implant infection. Materials and Methods: Searches of the US National Institutes of Health free digital archives of the biomedical and life sciences journal literature (PubMed) and The Cochrane Library of the Cochrane Collaboration (CENTRAL), as well as a hand search of other literature, were conducted to identify articles potentially relevant for the review. Randomized clinical trials, prospective cohort studies, longitudinal studies, case-control studies, and cross-sectional studies in humans reporting microbiologic findings in patients with diagnosed peri-implantitis were considered eligible for this review. Screening, data extraction, and quality assessment were conducted independently and in duplicate. Results: Twenty-one articles were eligible for inclusion in this review. Early studies focused on the identification of target periopathogens, whereas more recent studies used advanced molecular techniques for comprehensive overview of the peri-implantitis-associated microbiome. In summary, the microbiologic profile in peri-implantitis (1) is complex and variable, (2) consists of gram-negative anaerobic periopathogens and opportunistic microorganisms in almost the same ratio, (3) is frequently associated with the Epstein-Barr virus and nonsaccharolytic anaerobic gram-positive rods, (4) is not so strictly associated with Staphylococcus aureus, and (5) is different from that of periodontitis. A meta-analysis could not be performed because of the heterogeneity of the reviewed studies. Conclusion: Although a comparison of the published results was limited because of the inhomogeneity of the studies, it is clear that the microbiologic profile of peri-implantitis consists of aggressive and resistant microorganisms and is distinct from that of periodontitis. It seems that the quantitative characteristics of the microflora cohabitants represent the key determinant of disease, rather than the qualitative composition, which is very similar in healthy and peri-implantitis states. Keywords: bacteria, microbiota, peri-implantitis, periodontitis