Peri-implantitis, an inflammatory response around implants, has a poorly defined etiology and pathogenesis. To better understand the role of specific microorganisms in this disease process, clinical and microbiological parameters were examined in 24 patients with 98 osseointegrated implants. Sites were evaluated for probing depth (PD), plaque/calculus index (PI), gingival bleeding index (GBI), mobility, and crevicular fluid flow rate (CFFR). Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia in subgingival plaque were identified by latex agglutination assays. Clinically, a statistically significant correlation (P < 0.001) was observed between probing depth and the length of time an implant was present. Mobility was also significantly greater (P < 0.001) in the maxillary than in the mandibular implants. Subgingival sites harboring one of the three microorganisms had significantly greater PD, GBI, and CFFR than non-colonized sites. Implants in partially edentulous patients more frequently were colonized with P. gingivalis/P. intermedia than edentulous patients. The incidence of these microorganisms also correlated with fixture longevity. Implants present for 3 to 4 years had a significantly greater frequency of test microorganisms than implants present for 1 to 2 years. These findings suggest that microbial pathogens associated with periodontitis occur more commonly around implants exhibiting gingival inflammation (GBI) and may contribute to peri-implantitis.