The aim of the study was to evaluate the early colonization of non-submerged implants over a 6-month period in partially edentulous patients treated for advanced aggressive periodontal disease. In 22 patients treated for advanced aggressive periodontitis and in a supportive maintenance program for a period between 12 and 240 months at implant surgery, a total of 68 non-submerged dental implants were installed. Patients had a plaque score below 20%, and less than 20% of the pockets around the teeth were bleeding on probing (BOP). Using DNA-probes (micro-IDent), the presence and concentration of five periodontal pathogens (Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythensis (Tf) and Treponema denticola (Td)) were determined in the five deepest pockets of the rest dentition pre-operatively and after 6 months as well as five places around each implant 10 days, 1 month, 3 months and 6 months after surgery. In each patient, a test to determine the genotype interleukin-1 (IL-1) was performed (PST - micro-IDent). After 6 months, no difference in microbial composition as compared with baseline was found around the teeth in five patients, in 12 minute differences and in five patients important differences were observed. Ten days after surgery, three patients had a complete similar bacterial composition between teeth and implants. In 14 patients, the composition was fairly similar, while large differences in composition and concentration occurred in five patients. This microbiota around the implants remained almost unchanged over a 6-month period and did not hamper the clinical and radiographic osseointegration and did not lead to peri-implantitis, mucositis or initiation of bone destruction.