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Background: Oral microbiota has been at the center of cultural attention in recent years. In daily clinical practice, orthodontic appliances may be associated with an increased cariogenic risk and a worsening of preexisting periodontal diseases. Objective: The purpose of this review is to investigate the available evidence regarding the association between orthodontic appliances and changes in the quality and quantity of the oral microbiota. Design: The research included every article published up to October 2017 featuring the keywords ‘Orthodontic appliance* AND (microbiological colonization OR periodontal pathogen* OR Streptococcus mutans OR Lactobacillus spp. OR Candida OR Tannerella forsythia OR Treponema denticola OR Fusobacterium nucleatum OR Aggregatibacter actinomycetemcomitans OR Prevotella intermedia OR Prevotella nigrescens OR Porphyromonas gingivalis)’ and was conducted in the major medical databases. The methodological quality of selected papers was scored using the ‘Swedish Council on Technology Assessment in Health Care Criteria for Grading Assessed Studies’ (SBU) method. Results: Orthodontic appliances influence the oral microbiota with an increase in the counts of S. mutans and Lactobacillus spp. and in the percentage of potentially pathogenic gram-negative bacteria. Conclusions: There is moderate/high evidence regarding the association between orthodontic appliances and changes in the oral microbiota. PROSPERO registration number CRD42018091589.