BACKGROUND AND OBJECTIVE: Smoking is a recognized risk factor for peri-implant disease and leads to microbiological changes in mucositis and peri-implantitis. However, there is no knowledge about the impact of smoking in healthy peri-implant tissue. The aim of the study was to evaluate the microbiome in a peri-implant environment in smokers with healthy peri-implant conditions. METHODS: Peri-implant biofilm was collected around single clinically healthy, screwed-retained, teeth-surrounded implants in 12 non-smoker (NSMK) and 12 smoker (SMK) non-periodontitis subjects (no bleeding and probing depth <4 mm). Bacterial DNA was isolated and 16S ribosomal RNA gene libraries were sequenced using pyrosequencing, targeting the V3-V4 region. Datasets were processed using the Quantitative Insights into Microbial Ecology, Greengenes and the Human Oral Microbiome Database databases. RESULTS: An evident difference in the SMK peri-implant microbiome was observed compared to the NSMK microbiome, with a large abundance of species, even with a healthy peri-implant. The SMK core-microbiome showed an abundance of Fusobacterium, Tannerella and Mogibacterium, while the NSMK core revealed an abundance of Actinomyces, Capnocytophaga and Streptococcus, genera that are usually related to periodontal health. The microbiome inter-relationship was shown to be more inter-generic in SMK then in NSMK, indicating different microbiome cohesion. CONCLUSION: Smoking negatively affected the peri-implant microbiome, leading to a disease-associated state, even in clinically healthy individuals.