Objective: To determine the methodological quality of orthodontics clinical studies in six journals with the highest impact indexed by the Institute for Scientific Information (ISI), between January 2012 and December 2016. Methodology: We performed a systematic search in PubMed and we reviewed the abstract and methodology of all the selected studies. We classified as clinical trials the studies that evaluated the effectiveness of a treatment, comparing two or more interventions to a control group. Results: We reviewed 221 clinical trials with the MinCir scale. Regarding methodological quality average, the European Journal of Orthodontics showed the best average score (15.6 ± 2.83). Regarding continent results, Europe has the highest average score of methodological quality with 14.88 points. Conclusion:The methodological quality of the clinical trials in orthodontics indexed in ISI journals presented some deficiencies. Therefore, we suggest this information should be considered to analyze its implications for orthodontics practice.