BACKGROUND: The purpose of this longitudinal study was to determine the clinical status and the composition of the subgingival microbiota of dental implants and natural teeth in patients with a history of periodontitis. METHODS: Twenty-five partially edentulous patients treated for moderate to advanced adult periodontitis and having a total of 42 implants participated in this 3-year study. The assessment of clinical status was done 1, 2, and 3 years after prosthetic loading (T1, T2, and T3, respectively). Clinical parameters evaluated included probing depth (PD), clinical attachment level (CAL), gingival index (GI), and plaque index (PI). The subgingival microbiota at peri-implant and periodontal sites were analyzed at T1 and T2. RESULTS: No significant difference in clinical parameters between implants and teeth and within the 2 groups between different time points was observed through the study. PD and CAL measurements of sampled periodontal and peri-implant sites did not show any statistically significant difference through the study and between the 2 groups. PI of sampled periodontal sites showed a statistically significant improvement during the study. From the morphological observation of the subgingival microbiota, a significant difference in the composition of motile rods between implants and teeth was found at T1. There were no differences detected in the subgingival microbiota, culturally identified at peri-implant and periodontal sites for the duration of the study. CONCLUSIONS: In conclusion, implants were colonized by the indigenous periodontal microbiota and were well maintained in patients with a history of periodontitis. No significant association between progressing or non-progressing periodontal or peri-implant sampled sites in terms of loss of attachment and infection with at least one of the searched periodontal pathogens was found, suggesting that the presence of putative periodontopathogens at peri-implant and periodontal sites may not be associated with future attachment loss or implant failure.