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This study tested various protocols for bone decontamination after bacterial contact to determine if these treatments altered bone structure.Femurs from five Sprague-Dawley rats were sectioned and separated into eight groups. These were contaminated in a broth containing Pseudomonas aeroginosa and Staphylococcus aureus. Subsequently, the groups were treated with eight different decontamination regimens. A Scheffe's Grouping test was used to statistically compare the bacterial counts after each treatment protocol.Treatment with 4% chlorhexidine gluconate and 4% alcohol, Neosporin, cefazolin, and saline solution had little effect on bacterial growth. However, povidone-iodine, autoclaving, and ethyl alcohol with ethanol did significantly decrease the bacterial colony counts from the bone specimens. The autoclave and ethyl alcohol/ethanol induced changes in bony histologic examination.Results suggested that povidone-iodine decontaminates bone specimens without altering histologic conditions. Determination of successful grafting of bone treated with this protocol is required before its recommendation for clinical use.