The aim of this study was to evaluate qualitative differences in the subgingival microbiota at titanium implants, ad modum Brånemark, demonstrating clinical and radiographic signs of loss of supporting tissues (peri-implantitis) as compared to implants surrounded by healthy tissues. A total of 37 patients demonstrating 1 or more implants with bone loss > or = 3 threads, bleeding on probing and/or suppuration and 51 patients with clinically healthy mucosa and no bone loss were recruited for the study. In each patient subgingival bacterial samples were obtained using paper-points, and subjected to microbiological analysis by culture. The two types of clinical conditions showed distinct bacterial profiles. For implants with peri-implantitis putative periodontal pathogens, such as Porphyromonas gingivalis, Prevotella intermedia/Prevotella nigrescens and Actinobacillus actinomycetemcomitans, were found in 60% of the cases and microorganisms primarily not associated with periodontitis, such as Staphylococcus spp., enterics and Candida spp., were found in 55% of the peri-imaplant lesions. In contrast, implants surrounded by healthy tissue demonstrated a microbiota associated with periodontal health. The results indicate that the microbiota of the healthy peri-implant sulci is similar to that from corresponding conditions around teeth. However, in peri-implant areas staphylococci, enterics and yeasts were found almost as frequently as periopathogens indicating differences as compared to the microbiota around periodontitis affected teeth. A microbiological diagnosis may therefore be of guidance for the choice of antimicrobial treatment in patients with peri-implant infection.