This split-mouth study investigated the correlation of the qualitative and quantitative bacterial composition in dental plaque around clinically healthy periodontal and peri-implant subgingival sites with the levels of selected pro- and anti-inflammatory cytokines and the inflammatory infiltrate in the soft tissue surrounding a healthy dental implant and natural tooth in the same patient. Nine patients, all in good health and non-smokers, were studied. All of the patients were highly motivated in terms of oral hygiene and had healthy natural teeth and at least one healthy implant. After three sessions of professional oral care, clinical parameters were recorded. A sample of subgingival plaque was harvested with a sterile curette from the buccal side of the selected implants and teeth. The plaque samples were cultured to quantify the total microbiota and the number of obligate and facultative bacterial strains. Simultaneously, from the lingual/palatal aspect of the same implants and teeth the keratinized periodontal and peri-implant soft tissues were biopsied for cytokine expression and histomorphometric analysis. The tissue biopsies were halved: the real-time reverse transcriptase-polymerase chain reaction (PCR) was performed to detect active TNF-alpha, IL-1beta, IL-8, and TGF-beta2 and distribution, composition, quantification of inflammation were assessed in parallel. The patients harbored no periodontopathogens and the microbiological composition of the plaque taken from implant sites did not differ from that harvested from teeth. No significant differences were seen between implants and teeth for both proand anti-inflammatory cytokines. Even the histological examination showed no significant epithelial changes, although slight perivascular lymphocytic infiltration was seen in some biopsies.