Although some risk factors of peri-implant disease are well defined, the lack of efficient and predictable approaches to treat peri-implantitis has created difficulty in the management of those complications. The aim of this review was to evaluate the reliability of the diagnosis methods and to provide a set of guidelines to treat peri-implant diseases. A search of PubMed and a hand search of articles related to peri-implant diseases were conducted up to August 2013. A summary of the current methods for the diagnosis of peri-implantitis, its potential risk factors, and a flow chart to guide the clinical management of these conditions are presented.