The replacement of missing teeth with dental implants has been proved to have promising results and a high success rate. However, there have been increasing numbers of reports describing peri-implant diseases that are associated with this increased use of implants. Most studies investigated the peri-implantitis with marginal bone involved. Information of implant periapical lesion was insufficient by now. The purpose of this review article is to discuss the current knowledge including microbiological and histological analysis of apical peri-implant infection. The possible causes of apical peri-implant infection were investigated and correct diagnosis was made to assist clinicians in early treatment planning and prevention of the implant failure.