There is a lack of consensus guidelines for the decontamination of autogenous bone grafts after exposure to a nonsterile environment during graft contouring, intraoral bone harvesting, or when inadvertently dropped off the sterile field. Transplantation of contaminated bone may cause infectious complications or even augmentation failure. When selecting the antimicrobial agent of choice to treat harvested bone for transplantation purposes, focus should be placed on the safety of the agent towards bone and osteoprogenitor cells, maximum elimination of targeted pathogens that directly affect bone tissue, and a short exposure time. In systematically reviewing study results on the degree of bone graft contamination and the effects of decontamination methods, a protocol for decontamination of autogenous bone grafts is proposed. Among various decontamination agents investigated, 1% chlorhexidine proved highly effective (mean reduction of bacterial colony-forming units compared to saline solution: 99.97%). Minimum contact time required is 15 seconds and cell proliferation can be observed up to 30 seconds of exposure. The proposed decontamination protocol (1% chlorhexidine for 15 seconds) seems to represent a reasonable compromise in reference to sterility and cell viability. Comparative effectiveness research, however, is needed before clinical recommendations may be posed. Keywords: agent concentration, bone transplants, exposure time, graft decontamination, graft failure, graft infection