Purpose: To compare implants in healthy conditions and implants with peri-implantitis with regard to their clinical parameters and the microbiologic composition at the peri-implant sulcus, inside the implant connection, and the gingival sulcus of neighboring teeth. Materials and Methods: A cross-sectional study was performed including consecutive patients with implants in healthy conditions and with peri-implantitis. Clinical parameters for which patients were screened included bleeding on probing, pocket depth, and plaque index at six sites. Samples for microbiologic analysis were obtained from three locations: the peri-implant sulcus, inside the implant connection, and the gingival sulcus of neighboring teeth. Quantitative real-time polymerase chain reaction (PCR) was carried out for total counts of 10 microorganisms: Aggregatibacter actinomycetemcomitans, Porphyromona gingivalis, Tanerella forsythia, Tanerella denticola, Prevotela intermedia, Peptostreptococcus micros, Fusobacterium nucleatum, Campylobacter rectus, Eikenella corrodens, and Candida albicans. The response variables were the percentage of positive sites and total bacterial counts. Results: One hundred twenty-two implants in 57 patients were analyzed in the healthy group and 113 implants in 53 patients in the peri-implantitis group. Differences between the groups were statistically significant for bruxism, probing pocket depth, bleeding on probing, and radiographic bone level. Orange complex species (P intermedia, P micros, F nucleatum) were the most prevalent in the three types of sites for both groups, and prevalence values were higher in the peri-implantitis group. Differences in prevalence between groups were more marked inside the connection than in the peri-implant sulcus. Absolute loads of most microbes and total bacterial counts were higher for the peri-implantitis group in the three locations. Again, differences were bigger inside the connection than at the peri-implant sulcus. Significant interactions were found for prevalence and absolute microbial loads between groups and locations, and for the interaction of group × location. Conclusion: Clinical and microbiologic differences were observed between healthy subjects and those with peri-implantitis. Microbiologic differences between groups were more marked inside the connection than in the peri-implant sulcus. The potential role of the implant connection as a microbial reservoir for peri-implant diseases and in the outcome of their treatment should be confirmed with further studies. Schlagwörter: contamination of the implant connection, microbiologic contamination, peri-implantitis, periopathogen bacteria, RT-PCR