Most periodontal pathogens colonise different niches such as the oral mucosa, tongue, saliva, periodontal pockets, all hard intra-oral surfaces and the tonsils. Since intra-oral translocation of these pathogens between these niches is possible, a one stage disinfection of the whole mouth in one or two consecutive days as treatment strategy for periodontal infections must be considered. A one stage full-mouth disinfection is achieved by a scaling and root planing of all periodontal pockets within 24 hours, in combination with a chlorhexidine application in all niches (subgingival irrigation, mouth wash, brushing of the tongue, and spray for the pharynx). As such, reinfection by bacteria of recently instrumented sites is inhibited. This approach results in significant additional clinical and microbiological results compared to the classical approach (scaling and rootplaning per quadrant with several days or weeks between each session).