Peri-implant bone levels are influenced by pathologic and nonpathologic conditions. The understanding of peri-implant disease has evolved over the past several decades, and the classification of peri-implantitis has been limited to descriptions of disease progression or those involving soft and/or hard tissues (peri-implant mucositis or peri-implantitis). However, no classification system has been established based on etiology. The objective of this study was to identify various etiologies for peri-implantitis and to establish a classification system based on the pathogenesis. The results indicate that the majority of bone loss was related to biofilm, followed by iatrogenic factors, exogenous irritants, absence of keratinized tissue, and extrinsic pathology. The proposed classification system will allow the clinician to properly diagnose peri-implant diseases in relation to etiology. These conditions may respond differently to applied therapies.