A standard periodontal treatment consists of 4 to 6 scalings and root-planings at a 1- to 2-week interval, which allows reinfection of a previously disinfected area before completion of the treatment. The present pilot study aims to examine the microbiological long-term effects of a full-mouth disinfection. 10 patients with advanced chronic periodontitis were randomly allocated to a test and control group. The patients from the control group received scaling and root-planing and oral hygiene instructions at a 2-week interval. The full-mouth disinfection (test group) consisted of a full-mouth scaling and rootplaning in 2 visits within 24 h in combination with: tongue brushing with 1% chlorhexidine gel for 1 min, mouth rinsing with 0.2% chlorhexidine solution for 2 min and subgingival irrigation of all pockets (3x in 10 min) with 1% chlorhexidine gel. The patients of the test group were instructed to rinse 2x daily with 0.2% chlorhexidine. Plaque samples were taken at baseline and after 1, 2, 4 and 8 months. Differential phase-contrast microscopy showed a significantly larger reduction of spirochetes and motile organisms in the test group up to month 2 for the single-rooted and up to month 8 for the multi-rooted teeth. Furthermore, the culture data supported the effectiveness of the new treatment strategy. In both groups, the number of anaerobic CFU decreased 1 log around single- and 0.5 log around multi-rooted teeth. The number of anaerobic CFU remained low in the test group, in contrast to the control group. At 1 month, the test group harboured a significantly (p<0.01) lower proportion of pathogenic organisms, but this difference disappeared with time. Moreover, the test sites showed a significantly higher (p<0.02) increase in the proportion of beneficial micro-organisms up to 4 months. These findings suggest that a full-mouth disinfection leads to a significant microbiological improvement up to 2 months, which could be consolidated, although not significant, for the next 6 months.