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Aim The aim of this study was to analyze, by the aid of microbiological analysis and the field emission scanning electron microscopical (FE-SEM) analysis, the role of high-density polytetrafluoroethylene (d-PTFE) membranes in avoiding the microbial colonization of a nanocrystalline hydroxyapatite (nc-HA) bone graft and the involvement of this colonization in the healing process. Materials and methods Six patients underwent extraction of unrecoverable teeth, and a socket preservation technique was carried out with nc-HA synthetic bone graft and then covered with a d-PTFE membrane. After 28 days from surgery, FE-SEM analysis and BioTimer assay technique to assess the microbiological count of streptococci species were carried out. Data were collected and analyzed by the Student's t test (confidence interval: 95%). Results The mean amount of bacteria measured on the upper side of the membrane was 6.52 ± 0.50 CFU, while on the lower side, it was 6.59 ± 0.40 CFU. Significant differences were not found between the two sides of the membrane or between the different sectors (p > 0.05). The FE-SEM analysis revealed structured biofilms on both sides of the membrane: species of cocci, bacilli, and fusobacteria were recognizable in occasional settled vegetations. Conclusion Since the amount of bacteria found was low, the improved impermeability of the d-PTFE membrane permitted the healing process to proceed uneventful and without signs of infection or inflammation. Clinical relevance The infection of the graft site could lead to a failure of the socket preservation technique which could delay or compromise the rehabilitation following procedures. The use of d-PTFE can improve the bone regeneration thanks to its antimicrobial properties.