The increasing demand for clear aligners in orthodontics over the past decade reflects patients' preferences for simplicity and more comfortable treatment options. As clear aligners become more prevalent, there is a growing interest in understanding the physiological and microbial alterations accompanying their use. In light of these findings, it is crucial to guide orthodontists and general dentists in managing clear aligner cases regarding the impact on the risk of biofilm- induced oral diseases. Here, this master thesis is presented in chapters with the following aims: 1) perform a scoping review as a preliminary assessment of whether clear aligners are associated with a higher, lower, or similar risk of biofilm-related oral health issues such as dental caries and periodontal disease, and, 2) to investigate the microbiome change of clear aligners users as a relevant factor for caries development or periodontal diseases. As the methodology approached, the scooping review and cohort studies were performed according to the cited objectives. For the results, a collective of the literature showed a 58% similar risk of biofilm-inducing diseases for users of clear aligners and fixed appliances. For 17% of studies, clear aligners have shown reduced risk (chapter 1). 59% of these studies, considering clear aligner users, investigated periodontal diseases and the main biofilm-induced disease. In our clinical study, no significant differences were detected over time . At the genus level, after 30 days demonstrated significantly increased Bacillus abundance and decreased Prevotella abundance. Our results suggested that the general biodiversity and salivary microbial community structure did not change significantly and that patients had increased beneficial oral hygiene habits and awareness during the first six months of Invisalign treatment. (chapter 2). Key words: Orthodontics, Oral biofilms, Clear Aligners, Biofilm-related diseases.