The aim of this systematic review was to assess qualitative changes induced by fixed appliance orthodontic treatment on the subgingival microbiota. Seven databases were searched up to August 2017 for randomized and nonrandomized clinical studies assessing the effect of orthodontic appliances on the subgingival bacteria in human patients. After elimination of duplicate studies, data extraction and risk of bias assessment according to the Cochrane guidelines, random-effects meta-analyses of relative risks (RR) and their 95% confidence intervals (CIs) were performed. According to controlled studies, the presence of Aggregatibacter actinomycetemcomitans in the subgingival crevicular fluid of orthodontic patients was increased 3-6 months after fixed appliance insertion compared to untreated patients (2 studies; RR = 15.54; 95% CI = 3.19-75.85). There was still increased subgingival prevalence of Aggregatibacter actinomycetemcomitans (3 studies; RR = 3.98; 95% CI = 1.23-12.89) and Tannerella forsythia in orthodontic patients up to 6 months after appliance removal compared to untreated patients. However, caution is warranted due to high risk of bias and imprecision. Insertion of orthodontic fixed appliances seems to be associated with a qualitative change of subgingival microbiota, which reverts to some extent back to normal in the first months after appliance removal. However, there is limited evidence on the timing and extent of these changes.