Abstract Background Before implementing healthcare interventions, clinicians need to weigh the beneficial and adverse effects of interventions. However, a large body of evidence has demonstrated that seeking and reporting of adverse effects is suboptimal in clinical trials and in systematic reviews of interventions. This cross-sectional study will investigate the status of this problem in orthodontics. This study will assess whether adverse effects were sought and whether findings related to adverse effects were reported in systematic reviews of orthodontic interventions in the five leading orthodontic journals and in the Cochrane Database of Systematic Reviews. Methods Systematic reviews of clinical orthodontic interventions published between 01 August 2009 and 31 July 2019 in the five leading orthodontic journals and in the Cochrane Database will be included. Empty reviews will be excluded. The reporting of outcomes on adverse effects will not determine eligibility, i.e., reviews will not be excluded, because they did not report usable data. Study selection and data extraction will be conducted independently by two authors. Our primary outcome will be the prevalence of systematic reviews of orthodontic interventions that sought any findings related to adverse effects in the included studies. Additional prevalence statistics will be calculated on a series of items related to seeking of adverse effects in the eligible reviews. All statistics will be calculated for (1) all journals together, (2) the group of five orthodontic journals and the Cochrane Database of Systematic Reviews separately, and (3) each individual journal separately. Chi-square tests of independence will be used to compare these groups. Discussion This study will assess whether adverse effects were sought in systematic reviews of orthodontic interventions. This knowledge is important, because reviews that present an incomplete picture on adverse effects can have unfavorable consequences for the end-users. Also not reporting that no adverse effects were assessed in eligible studies included in a systematic review can mislead pertinent stakeholders. Our findings could have policy implications for making judgments on accepting or rejecting an intervention systematic review for publication, for example, by directing editors and peer-reviewers to adopt the various items on adverse effects defined in the MECIR standards and in the PRISMA harm checklist.