Dental implant surgery produces bone debris that can be used in the "simultaneous augmentation" technique. Although this debris is contaminated with oral bacteria, a stringent aspiration protocol has been shown to reduce the levels of contamination. Chlorhexidine mouthrinse is a well-proven antibacterial rinse that has been shown to reduce infectious complications associated with dental implants. This study examined the effect of pre-operative rinsing with a 0.1% chlorhexidine digluconate mouthrinse on the bacterial contaminants present in collected bone debris bone (CBD). Twenty partially edentate patients were randomly allocated into equal groups and underwent bone collection using the Frios Bone Collector (FBC) during the insertion of two dental implants. In group T a pre-operative chlorhexidine rinse was used, whilst in group C sterile water was used. For both groups, a stringent bone collection protocol was used. Bone samples were immediately transported for microbial analysis. Colonial and microscopic morphology, gaseous requirements and identification kits were utilised for identification of the isolated microbes. Thirty-nine species were identified including a number associated with disease, in particular Actinomyces odontolyticus, Clostridium bifermentans, Prevotella intermedia, and Propionibacterium propionicum. Samples from group T (chlorhexidine mouthrinse) yielded significantly fewer organisms (P < 0.001) than in group C (sterile water mouthrinse). Gram-positive cocci dominated the isolates from both groups. It is concluded that if bone debris is to be used for the purpose of immediate simultaneous augmentation, a preoperative chlorhexidine mouthrinse should be utilised in conjunction with a stringent aspiration protocol to reduce further the bacterial contamination of CBD.