Autogenous bone particles can be obtained with bone collectors during implant osteotomy; however, collected bone particles contain oral microorganisms that may cause infectious complications. The purpose of this review was to summarize the clinical studies that have evaluated the degree of this contamination and the effectiveness of different decontamination methods. Stringent aspiration protocol, preoperative oral chlorhexidine rinse, and antibiotic prophylaxis are important precautions to be implemented when collected bone particles are to be implanted. Despite reducing contamination of collected bone particles, none of the methods described in the literature can completely decontaminate collected bone particles or prevent the risk of infectious complications. Further research is needed to identify more effective decontamination methods.