BACKGROUND: Peri-implant diseases include peri-implant mucositis, describing an inflammatory lesion of the peri-implant mucosa, and peri-implantitis, which also includes loss of supporting bone. METHODS: A literature search of the Medline database (Ovid), up to 21 January 2008 was carried out using a systematic approach, in order to review the evidence for diagnosis and the risk indicators for peri-implant diseases. RESULTS: Experimental and clinical studies have identified various diagnostic criteria including probing parameters, radiographic assessment and peri-implant crevicular fluid and saliva analyses. Cross-sectional analyses have investigated potential risk indicators for peri-implant disease including poor oral hygiene, smoking, history of periodontitis, diabetes, genetic traits, alcohol consumption and implant surface. There is evidence that probing using a light force (0.25 N) does not damage the peri-implant tissues and that bleeding on probing (BOP) indicates presence of inflammation in the peri-implant mucosa. The probing depth, the presence of BOP, and suppuration should be assessed regularly for the diagnosis of peri-implant diseases. Radiographs are required to evaluate supporting bone levels around implants. The review identified strong evidence that poor oral hygiene, a history of periodontitis and cigarette smoking, are risk indicators for peri-implant disease. Future prospective studies are required to confirm these factors as true risk factors.