OBJECTIVE: The aim of this in vivo study was to evaluate two different types of implant-abutment connections: screwed connection and cemented connection, analyzing peri-implant bacteria microflora as well as other clinical parameters. PATIENTS AND METHODS: Twenty implants were selected, inserted in 20 patients, 10 with a screwed implant-abutment connection (Group 1) and 10 with a cemented implant-abutment connection (Group 2). The peri-implant microflora was collected, after at least 360 days from the prosthetic rehabilitation, using paper points inserted in peri-implant sulcus for 30 s. Polymerase chain reaction (PCR) Real-time analyzed the presence of 9 bacteria periodontal-pathogens and Candida albicans. RESULTS: Our findings showed that bacteria colonized all Groups analyzed, the average bacterial count was 3.7 E + 08 (+/- 1.19) in Group 1, compared to 2.1 E + 08 (+/- 0.16) in Group 2; no statistically significant differences were observed (p >0.0.5). In Group 1, however, bacterial colonization of peri-implant sulci was over the pathogenic threshold for 5 bacteria, indicating a high-risk of peri-implantitis. Also in Group 2, results showed a microflora composed by all bacteria analyzed but, in this case, bacterial colonization of peri-implant sulci was over the pathogenic threshold for only 1 bacterium, indicating a lower risk of peri-implantitis. Moreover, clinical parameters (PPD >3 mm and m SBI >0) confirmed a greater risk of peri-implantitis in Group 1 compared to Group 2 (p < 0.05). CONCLUSIONS: We concluded that, also after only 360 days, implants with screwed connection showed a higher risk of peri-implantitis that implants with cemented connection.