The purpose of this study was to investigate the possibility of antimicrobial treatment of peri-implant infections associated with a periodontitis-like subgingival microbiota. Nine partially or fully edentulous patients with titanium hollow cylinder implants were selected which showed loss of bone and probing depths > or = 5 mm on one or several implants after at least 6 months following installation. They also yielded subgingival microbial samples with > or = 10(6) CFU/ml, including > or = 20% gram-negative anaerobic bacteria. The treatment included mechanical cleaning, irrigation of all peri-implant pockets > 3 mm with 0.5% chlorhexidine and systemic antimicrobial therapy (1000 mg ornidazole for 10 consecutive days). After therapy, bleeding scores decreased immediately and, over a one-year observation period, remained significantly lower than before treatment. A significant gradual reduction in mean probing depths was detected over this one-year period; only one case showed no improvement of local probing depth. Microbiological parameters indicated an instantaneous quantitative and qualitative change following treatment. Subsequently, several of these parameters tended to shift back towards pretreatment values. In the second half of the observation period, however, this tendency was reversed, and levels significantly different from baseline were eventually established. This study demonstrated that treatment aiming at reducing the subgingival bacterial mass and suppressing the anaerobic segment had a beneficial effect in patients suffering from peri-implantitis.