Although the infectious initiation of peri-implantitis is commonly accepted, differences in microbial composition in peri-implantitis and periodontitis has been the subject of some debate. The presence of periodontal pathogens at sites with peri-implantitis has been documented by many studies. However, other studies have revealed that sites with peri-implantitis harbour high levels of microorganisms which have not primarily been associated with periodontitis, such as Candida-, Staphylococcus- and Enterobacteriaceae species. These findings suggest that peri-implantitis may display a flora distinct from that of periodontitis. The aim of the present study was to evaluate the presence of three known periodontal pathogens, Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans), Porphyromonas gingivalis (P. gingivalis) and Treponema denticola (T. denticola) at healthy and diseased (peri-implantitis) sites. A second aim was to evaluate the presence of Candida-, Staphylococcus- and Enterobacteriaceae-species at the same sites. The hypothesis was that A. actinomycetemcomitans, P. gingivalis, T. denticola, Candida-, Staphylococcus- and Enterobacteriaceae-species would be detected at higher levels in peri-implantitis samples than healthy controls. Samples of peri-implant crevicular fluid (PICF) were obtained from peri-implant pockets in 13 subjects, of which 5 subjects had both healthy and diseased implants, 4 subjects had healthy implants only and the remaining 4 had only diseased implants. Microbial analyses were carried out using Real Time PCR and microbial culture techniques. A. actinomycetemscomitans, P. gingivalis and T. denticola were detected at higher levels at sites with peri-implantitis compared to healthy sites. Furthermore, Klebsiella oxytoca was detected in one peri-implantitis sample whereas Candida- and Staphylococcus species were not detected in any of the samples. Higher counts of periodontal pathogens were detected around implants with peri-implantitis. The suggestion that Candida and Staphylococcus may be present at higher levels in peri-implantitis was not supported by this study as these bacteria could not be detected in any of the samples.